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ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE 40 (JUN) 280-288 (1984)
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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 105 (18): 5761-5766 1983
PROTEIN-STRUCTURE ALIGNMENT
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ELECTRONIC DISTRIBUTIONS WITHIN PROTEIN PHENYLALANINE AROMATIC RINGS ARE REFLECTED BY THE 3-DIMENSIONAL OXYGEN ATOM ENVIRONMENTS
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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES 79 (16): 4843-4847 1982
PROTEIN MOTIFS AND DATA-BASE SEARCHING
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ORIGIN OF HYDROGEN-BONDING - ENERGY DECOMPOSITION STUDY
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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 99 (5): 1316-1332 1977
LONE-PAIR DIRECTIONALITY IN HYDROGEN-BOND POTENTIAL FUNCTIONS FOR MOLECULAR MECHANICS CALCULATIONS - THE INHIBITION OF HUMAN CARBONIC ANHYDRASE-II BY SULFONAMIDES
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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 107 (25): 7653-7658 1985
THE EXACT MULTICENTER MULTIPOLAR PART OF A MOLECULAR CHARGE-DISTRIBUTION AND ITS SIMPLIFIED REPRESENTATIONS
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SUGAR AND SIGNAL-TRANSDUCER BINDING-SITES OF THE ESCHERICHIA-COLI GALACTOSE CHEMORECEPTOR PROTEIN
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CRYSTAL-STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 OF V-SRC COMPLEXED WITH TYROSINE-PHOSPHORYLATED PEPTIDES
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SURVEY OF AMINO-ACID SIDE-CHAIN INTERACTIONS IN 21 PROTEINS
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JOURNAL OF MOLECULAR BIOLOGY 118 (3): 289-304 1978
SEQUENCE AND STRUCTURE OF YEAST PHOSPHOGLYCERATE KINASE
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STRUCTURE OF A COMPLEX OF CATABOLITE GENE ACTIVATOR PROTEIN AND CYCLIC-AMP REFINED AT 2.5 A RESOLUTION
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JOURNAL OF MOLECULAR BIOLOGY 198 (2): 311-326 NOV 20 1987
A NEW FORCE-FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC-ACIDS AND PROTEINS
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Die Ammoniumsalze als einfachste Metallammoniake
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MOLECULAR PHYSICS 79 (3): 597-610 JUN 20 1993
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TI: FIRST-ORDER COULOMB INTERACTION ENERGIES FOR ATOMS AND DIATOMIC-MOLECULES
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JN: MOLECULAR PHYSICS, 1995, Vol.86, No.3, pp.443-465
A NEW DISTRIBUTED MULTIPOLE PROCEDURE FOR LINEAR-MOLECULES
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CHEMICAL PHYSICS LETTERS 208 (3-4): 159-166 JUN 11 1993
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TI: A SYSTEMATIC MODEL POTENTIAL FOR LI+-H2O
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ON THE RELATIONSHIP BETWEEN 1ST-ORDER EXCHANGE AND COULOMB INTERACTION ENERGIES FOR CLOSED-SHELL ATOMS AND MOLECULES
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MOLECULAR PHYSICS 79 (2): 253-275 JUN 10 1993
A SYSTEMATIC INTERMOLECULAR POTENTIAL METHOD APPLIED TO CHLORINE
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MOLECULAR PHYSICS 71 (6): 1381-1404 DEC 20 1990
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MOLECULAR PHYSICS 69 (3): 507-533 FEB 20 1990
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WILLIAMS DE, COX SR
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE 40 (AUG): 404-417 1984
AN UNLIKELY SUGAR SUBSTRATE SITE IN THE 1.65 ANGSTROM STRUCTURE OF THE HUMAN ALDOSE REDUCTASE HOLOENZYME IMPLICATED IN DIABETIC COMPLICATIONS
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STRUCTURE OF PHOSPHATE-FREE RIBONUCLEASE-A REFINED AT 1.26 A
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BIOCHEMISTRY 27 (8): 2705-2717 APR 19 1988
2.2-ANGSTROM REFINED CRYSTAL-STRUCTURE OF THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN-KINASE COMPLEXED WITH MNATP AND A PEPTIDE INHIBITOR
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ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 49: 362-365 Part 3, MAY 1 1993
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TI: APPROXIMATE DENSITY FUNCTIONAL THEORY AS A PRACTICAL TOOL IN
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AU: ZIEGLER_T
JN: CHEMICAL REVIEWS, 1991, Vol.91, No.5, pp.651-667
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TI: AROMATIC HYDROGEN-BOND IN SEQUENCE-SPECIFIC PROTEIN-DNA
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AU: PARKINSON_G, GUNASEKERA_A, VOJTECHOVSKY_J, ZHANG_XP, KUNKEL_TA,
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JN: NATURE STRUCTURAL BIOLOGY, 1996, Vol.3, No.10, pp.837-841
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TI: PROTEIN SECONDARY STRUCTURAL TYPES ARE DIFFERENTIALLY CODED ON
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JN: PROTEIN SCIENCE, 1996, Vol.5, No.10, pp.1973-1983
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HOW STRONG IS A PI-FACIAL HYDROGEN BOND?
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TI: A TEST OF THE JIGSAW PUZZLE MODEL FOR PROTEIN-FOLDING BY
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AU: GASSNER_NC, BAASE_WA, MATTHEWS_BW
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
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TI: CATION-PI INTERACTIONS IN AROMATICS OF BIOLOGICAL AND MEDICINAL
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AU: MECOZZI_S, WEST_AP, DOUGHERTY_DA
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
STATES OF AMERICA, 1996, Vol.93, No.20, pp.10566-10571
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TI: EFFECTS OF MONOMER GEOMETRY AND BASIS-SET SATURATION ON COMPUTED
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AU: MAS_EM, SZALEWICZ_K
JN: JOURNAL OF CHEMICAL PHYSICS, 1996, Vol.104, No.19, pp.7606-7614
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TI: DISSOCIATION-ENERGY OF THE BENZENE WATER VAN-DER-WAALS COMPLEX
AU: CHENG_BM, GROVER_JR, WALTERS_EA
JN: CHEMICAL PHYSICS LETTERS, 1995, Vol.232, No.4, pp.364-369
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TI: BENZENE DIMER - A GOOD MODEL FOR PI-PI INTERACTIONS IN PROTEINS - A
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JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, Vol.118, No.45,
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TI: SOLUTION STRUCTURE OF A BIOLOGICALLY-ACTIVE CYCLIC LDV PEPTIDE ANALOG
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AU: DOYLE_PM, HARRIS_JC, MOODY_CM, SADLER_PJ, SIMS_M, THORNTON_JM,
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JN: INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH, 1996, Vol.47,
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TI: TOWARDS MEETING THE PARACELSUS CHALLENGE - THE DESIGN, SYNTHESIS, AND
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JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1996, Vol.24, No.4, pp.502-
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TI: From Levinthal to pathways to funnels
AU: Dill_KA, Chan_HS
JN: NATURE STRUCTURAL BIOLOGY, 1997, Vol.4, No.1, pp.10-i9
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TI: Multiconformational NMR analysis of sandostatin (octreotide):
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TI: PRO-LIGAND - AN APPROACH TO DE-NOVO MOLECULAR DESIGN .4. APPLICATION
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JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1995, Vol.9, No.3,
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TI: PRO-LIGAND - AN APPROACH TO DE-NOVO MOLECULAR DESIGN .6. FLEXIBLE
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JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1995, Vol.9, No.5,
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TI: THE COMPUTER-PROGRAM LUDI - A NEW METHOD FOR THE DENOVO DESIGN OF
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AU: BOHM_HJ
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1992, Vol.6, No.1, pp.61-
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TI: ON THE ELECTROSTATIC AND STERIC SIMILARITY OF LACTAM COMPOUNDS AND
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AU: FRAU_J, PRICE_SL
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1996, Vol.10, No.2,
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TI: Three-dimensional hydrogen-bond geometry and probability
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JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1996, Vol.10, No.6,
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TI: The measurement of molecular diversity: A three-dimensional
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JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1996, Vol.10, No.6,
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TI: STRUCTURE-GUIDED ANALYSIS REVEALS 9 SEQUENCE MOTIFS CONSERVED AMONG
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JN: JOURNAL OF MOLECULAR BIOLOGY, 1995, Vol.253, No.4, pp.618-632
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TI: STRUCTURE AND FUNCTION OF DNA METHYLTRANSFERASES
AU: CHENG_XD
JN: ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 1995, Vol.24,
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TI: UNIVERSAL CATALYTIC DOMAIN-STRUCTURE OF ADOMET-DEPENDENT
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JN: JOURNAL OF MOLECULAR BIOLOGY, 1995, Vol.247, No.1, pp.16-20
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TI: STRUCTURE-BASED DRUG DESIGN
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JN: NATURE, 1996, Vol.384, No.6604 SS, pp.23-26
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TI: MONSSTER: A method for folding globular proteins with a small
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TI: LINGUISTIC COMPLEXITY OF PROTEIN SEQUENCES AS COMPARED TO TEXTS OF
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JN: BIOSYSTEMS, 1996, Vol.38, No.1, pp.65-74
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JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
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TI: SYMMETRY IN CHEMISTRY FROM THE HYDROGEN-ATOM TO PROTEINS
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TI: EMPIRICAL FREE-ENERGY CALCULATIONS OF LIGAND-PROTEIN CRYSTALLOGRAPHIC
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TI: A NEW APPROACH TO PROTEIN FOLD RECOGNITION
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TI: CALCULATION OF CONFORMATIONAL ENSEMBLES FROM POTENTIALS OF MEAN FORCE
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TI: Structure-based design of a constrained peptide mimic of the
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TI: Molecular docking to ensembles of protein structures
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TI: STATISTICAL POTENTIALS EXTRACTED FROM PROTEIN STRUCTURES - HOW
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TI: A PREFERENCE-BASED FREE-ENERGY PARAMETERIZATION OF ENZYME-INHIBITOR
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JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.267, No.3, pp.727-748
(9760)
TI: PROMISE: A new database of information on prosthetic centres and
metal ions in protein active sites
AU: Degtyarenko_KN, North_ACT, Findlay_JBC
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.3, pp.183-186
(9761)
TI: ISOLATION OF A CANDIDATE REPRESSOR ACTIVATOR, NF-E1 (YY-1, DELTA),
THAT BINDS TO THE IMMUNOGLOBULIN KAPPA-3' ENHANCER AND THE
IMMUNOGLOBULIN HEAVY-CHAIN MU-E1 SITE
AU: PARK_K, ATCHISON_ML
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES
OF AMERICA, 1991, Vol.88, No.21, pp.9804-9808
(9762)
TI: TRANSCRIPTIONAL REPRESSION BY YY1, A HUMAN GLI-KRUPPEL-RELATED
PROTEIN, AND RELIEF OF REPRESSION BY ADENOVIRUS E1A PROTEIN
AU: SHI_Y, SETO_E, CHANG_LS, SHENK_T
JN: CELL, 1991, Vol.67, No.2, pp.377-388
(9763)
TI: CATION-PI BONDING AND AMINO-AROMATIC INTERACTIONS IN THE BIOMOLECULAR
RECOGNITION OF SUBSTITUTED AMMONIUM LIGANDS
AU: SCRUTTON_NS, RAINE_ARC
JN: BIOCHEMICAL JOURNAL, 1996, Vol.319, No.Pt1, pp.1-8
(9764)
TI: CORRELATION OF THE HYDROGEN-BOND ACCEPTOR PROPERTIES OF NITROGEN WITH
THE GEOMETRY OF THE NSP(2)-]NSP(3) TRANSITION IN R(1)(X=)C-NR(2)R(3)
SUBSTRUCTURES - REACTION PATHWAY FOR THE PROTONATION OF NITROGEN
AU: ALLEN_FH, BIRD_CM, ROWLAND_RS, HARRIS_SE, SCHWALBE_CH
JN: ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 1995, Vol.51,
No.Pt6, pp.1068-1081
(9765)
TI: MOLECULAR-DYNAMICS POTENTIAL OF MEAN FORCE CALCULATIONS - A STUDY OF
THE TOLUENE-AMMONIUM PI-CATION INTERACTIONS
AU: CHIPOT_C, MAIGRET_B, PEARLMAN_DA, KOLLMAN_PA
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, Vol.118, No.12,
pp.2998-3005
(9766)
TI: Enzymes and symmetrical molecules
AU: Barry_JM
JN: TRENDS IN BIOCHEMICAL SCIENCES, 1997, Vol.22, No.6, pp.228-230
(9767)
TI: Comparison of van der Waals and semiempirical calculations of
the molecular volumes of small molecules and proteins
AU: Rellick_LM, Becktel_WJ
JN: BIOPOLYMERS, 1997, Vol.42, No.2, pp.191-202
(9768)
TI: A method to search for similar protein local structures at ligand-
binding sites and its application to adenine recognition
AU: Kobayashi_N, Go_N
JN: EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 1997, Vol.26,
No.2, pp.135-144
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TI: Conformational analysis of dipeptide mimetics
AU: Gillespie_P, Cicariello_J, Olson_GL
JN: BIOPOLYMERS, 1997, Vol.43, No.3, pp.191-217
(9771)
TI: ZINC MINING FOR PROTEIN DOMAINS
AU: SCHWABE_JWR, KLUG_A
JN: NATURE STRUCTURAL BIOLOGY, 1994, Vol.1, No.6, pp.345-349
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TI: Experimental evidence at atomic resolution for intramolecular N-H
center dot center dot center dot pi (Phenyl) interactions in a family
of amino acid derivatives
AU: Crisma_M, Formaggio_F, Valle_G, Toniolo_C, Saviano_M, Iacovino_R,
Zaccaro_L, Benedetti_E
JN: BIOPOLYMERS, 1997, Vol.42, No.1, pp.1-6
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TI: PRO-D-NME-AMINO ACID AND D-PRO-NME-AMINO ACID - SIMPLE, EFFICIENT
REVERSE-TURN CONSTRAINTS
AU: CHALMERS_DK, MARSHALL_GR
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, Vol.117, No.22,
pp.5927-5937
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TI: BALI: Automatic assignment of bond and atom types for protein
ligands in the PDB
AU: Hendlich_M, Rippmann_F, Barnickel_G
JN: J. CHEM. INF. COMPUT. SCI., 1997, Vol.37, No.4, pp.774-778
(9775)
TI: SHAPING UP TO PROTEINS
AU: EGGLESTON_IM, MUTTER_M
JN: CHEMISTRY IN BRITAIN, 1996, Vol.32, No.5, pp.39-41
(9776)
TI: Protein thermal stability: hydrogen bonds or internal packing?
AU: Vogt_G, Argos_P
JN: FOLDING & DESIGN, 1997, Vol.2, No.4, pp.S40-S46
(9777)
TI: KNOWLEDGE-BASED POTENTIALS FOR PROTEINS
AU: SIPPL_MJ
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1995, Vol.5, No.2, pp.229-235
(9778)
TI: An electrophile-nucleophile interaction in metalloprotein structures
AU: Chakrabarti_P, Pal_D
JN: PROTEIN SCIENCE, 1997, Vol.6, No.4, pp.851-859
(9779)
TI: Tertiary structure prediction using mean-force potentials and
internal energy functions: successful prediction for coiled-coil
AU: ODonoghue_SI, Nilges_M
JN: FOLDING & DESIGN, 1997, Vol.2, No.4, pp.S47-S52
(9780)
TI: Ambiguous distance data in the calculation of NMR structures
AU: Nilges_M
JN: FOLDING & DESIGN, 1997, Vol.2, No.4, pp.S53-S57
(9781)
TI: Design of peptides, proteins, and peptidomimetics in chi space
AU: Hruby_VJ, Li_GG, HaskellLuevano_C, Shenderovich_M
JN: BIOPOLYMERS, 1997, Vol.43, No.3, pp.219-266
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TI: HELMHOLTZ FREE-ENERGY OF PEPTIDE HYDROGEN-BONDS IN PROTEINS
AU: SIPPL_MJ
JN: JOURNAL OF MOLECULAR BIOLOGY, 1996, Vol.260, No.5, pp.644-648
(9783)
TI: HYDROGEN-BONDING AND MOLECULAR-SURFACE SHAPE COMPLEMENTARITY AS
A BASIS FOR PROTEIN DOCKING
AU: MEYER_M, WILSON_P, SCHOMBURG_D
JN: JOURNAL OF MOLECULAR BIOLOGY, 1996, Vol.264, No.1, pp.199-210
(9784)
TI: Assembly of protein tertiary structures from fragments with similar
local sequences using simulated annealing and Bayesian scoring
functions
AU: Simons_KT, Kooperberg_C, Huang_E, Baker_D
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.268, No.1, pp.209-225
(9785)
TI: Determination of atomic desolvation energies from the structures of
crystallized proteins
AU: Zhang_C, Vasmatzis_G, Cornette_JL, DeLisi_C
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.267, No.3, pp.707-726
(9786)
TI: Protein thermal stability, hydrogen bonds, and ion pairs
AU: Vogt_G, Woell_S, Argos_P
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.269, No.4, pp.631-643
(9787)
TI: Analysis of protein-protein interactions and the effects of
amino acid mutations on their energetics. The importance of
water molecules in the binding epitope
AU: Covell_DG, Wallqvist_A
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.269, No.2, pp.281-297
(9788)
TI: Electrostatics and hydration at the homeodomain-DNA interface:
Chemical probes of an interfacial water cavity
AU: Labeots_LA, Weiss_MA
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.269, No.1, pp.113-128
(9789)
TI: Automated NOESY interpretation with ambiguous distance
restraints: The refined NMR solution structure of the
pleckstrin homology domain from beta-spectrin
AU: Nilges_M, Macias_MJ, ODonoghue_SI, Oschkinat_H
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.269, No.3, pp.408-422
(9790)
TI: Prediction of protein side-chain conformations by principal component
analysis for fixed main-chain atoms
AU: Ogata_K, Umeyama_H
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.4, pp.353-359
(9791)
TI: Assessment of pseudo-energy potentials by the best-five test: A
new use of the three-dimensional profiles of proteins
AU: Ota_M, Nishikawa_K
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.4, pp.339-351
(9792)
TI: Accurate ab initio quantum chemical determination ... and
assesment of empirical force fields
AU: Beachy_MD, Chasman_D, Murphy_RB, Halgren_TA, Friesner_RA
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1997, Vol.119 pp.5908-5920
(9793)
TI: The 'Asx-Pro turn' as a local structural motif stabilized by
alternative patterns of hydrogen bonds and a consensus-derived model
of the sequence Asn-Pro-Asn
AU: Wilson_DR, Finlay_BB
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.5, pp.519-529
(9794)
TI: The structural basis of protein folding
AU: Dobson_CM
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.SS, p.19
(9795)
TI: How hydrogen bonds break: A molecular dynamics study of
fluctuations and unfolding events in human lysozyme.
AU: Buck_M, Karplus_M
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.SS, p.22
(9796)
TI: Molecular orbital studies on modified ribozyme reactions
AU: Kinoshita_H, Shimizu_K
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.SS, p.64
(9798)
TI: Determination of the relative configuration of organic compounds
using NMR and DG: A systematic approach for a model system
AU: Kock_M, Junker_J
JN: JOURNAL OF MOLECULAR MODELING, 1997, Vol.3, No.9, pp.403-407
(9799)
TI: Molecular dynamics simulations of zinc ions in water using CHARMM
AU: Obst_S, Bradaczek_H
JN: JOURNAL OF MOLECULAR MODELING, 1997, Vol.3, No.6, pp.224-232
(97100)
TI: The Molecular Mechanics of Quantized Valence Bonds
AU: Box_VGS
JN: JOURNAL OF MOLECULAR MODELING, 1997, Vol.3, No.3, pp.124-141
(97101)
TI: Science and God: A warming trend?
AU: Easterbrook_G
JN: SCIENCE, 1997, Vol.277, No.5328, pp.890-893
(97102)
TI: Chemical physics - A quick look at hydrogen bonds
AU: Douhal_A
JN: SCIENCE, 1997, Vol.276, No.5310, pp.221-222
(97103)
TI: X-H center dot center dot center dot pi(phenyl) interactions -
Theoretical and crystallographic observations
AU: Malone_JF, Murray_CM, Charlton_MH, Docherty_R, Lavery_AJ
JN: JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS, 1997, Vol.93,
No.19, pp.3429-3436
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TI: Protein folding and the paracelsus challenge
AU: Rose_GD
JN: NATURE STRUCTURAL BIOLOGY, 1997, Vol.4, No.7, pp.512-514
(97105)
TI: Protein alchemy: Changing beta-sheet into alpha-helix
AU: Dalal_S, Balasubramanian_S, Regan_L
JN: NATURE STRUCTURAL BIOLOGY, 1997, Vol.4, No.7, pp.548-552
(97106)
TI: Evolutionary chemistry: Getting there from here
AU: Joyce_GF
JN: SCIENCE, 1997, Vol.276, No.5319, pp.1658-1659
(97107)
TI: Structural insights into the evolution of an antibody combining site
AU: Wedemayer_GJ, Patten_PA, Wang_LH, Schultz_PG, Stevens_RC
JN: SCIENCE, 1997, Vol.276, No.5319, pp.1665-1669
(97108)
TI: Is the parallel or antiparallel beta-sheet more stable? A
semiempirical study
AU: Gailer_C, Feigel_M
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1997, Vol.11, No.3,
pp.273-277
(97109)
TI: An automated method for predicting the positions of hydrogen-
bonding atoms in binding sites
AU: Mills_JEJ, Perkins_TDJ, Dean_PM
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1997, Vol.11, No.3,
pp.229-242
(97110)
TI: CAMDAS: An automated conformational analysis system using
molecular dynamics
AU: Tsujishita_H, Hirono_S
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1997, Vol.11, No.3,
pp.305-315
(97111)
TI: Residual colours: a proposal for aminochromography
AU: Taylor_WR
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.7, pp.743-746
(97112)
TI: Design of two-helix motifs in peptides: crystal structure of a system
of linked helices of opposite chirality and a model helix-linker
peptide
AU: Karle_IL, Banerjee_A, Balaram_P
JN: FOLDING & DESIGN, 1997, Vol.2, No.4, pp.203-210
(97113)
TI: ALTERNATIVE APPROACHES TO POTENTIAL OF MEAN FORCE CALCULATIONS -
FREE-ENERGY PERTURBATION VERSUS THERMODYNAMIC INTEGRATION - CASE-
STUDY OF SOME REPRESENTATIVE NONPOLAR INTERACTIONS
AU: CHIPOT_C, KOLLMAN_PA, PEARLMAN_DA
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1996, Vol.17, No.9, pp.1112-1131
(97114)
TI: A density functional study of the glycine molecule: Comparison with
post-Hartree-Fock calculations and experiment
AU: Nguyen_DT, Scheiner_AC, Andzelm_JW, Sirois_S, Salahub_DR, Hagler_AT
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.13, pp.1609-1631
(97115)
TI: Electrostatics of proteins: Description in terms of two
dielectric constants simultaneously
AU: Krishtalik_LI, Kuznetsov_AM, Mertz_EL
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.28, No.2,
pp.174-182
(97116)
TI: The foldability landscape of model proteins
AU: Govindarajan_S, Goldstein_RA
JN: BIOPOLYMERS, 1997, Vol.42, No.4, pp.427-438
(97117)
TI: Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with
alkanol hydroxyl groups
AU: Lommerse_JPM, Price_SL, Taylor_R
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.6, pp.757-774
(97118)
TI: Self-consistent field approach to protein structure and
stability .1. pH dependence of electrostatic contribution
AU: Dimitrov_RA, Crichton_RR
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.27, No.4,
pp.576-596
(97119)
TI: DESIGN OF A MONOMERIC 23-RESIDUE POLYPEPTIDE WITH DEFINED TERTIARY
STRUCTURE
AU: STRUTHERS_MD, CHENG_RP, IMPERIALI_B
JN: SCIENCE, 1996, Vol.271, No.5247, pp.342-345
(97120)
TI: De novo protein design: Fully automated sequence selection
AU: Dahiyat_BI, Mayo_SL
JN: SCIENCE, 1997, Vol.278, No.5335, pp.82-87
(97121)
TI: Proteins from scratch
AU: DeGrado_WF
JN: SCIENCE, 1997, Vol.278, No.5335, pp.80-81
(97122)
TI: Generation of pseudonative protein structures for threading
AU: Hamprecht_FA, Scott_W, vanGunsteren_WF
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.28, No.4, pp.522-
529
(97123)
TI: Predictions of peptide and protein backbone structural parameters
from first principles .4. Systematic comparisons of calculated N-
C(alpha)-C' angles with peptide crystal structures
AU: Jiang_XQ, Cao_M, Newton_SQ, Schafer_L
JN: ELECTRONIC JOURNAL OF THEORETICAL CHEMISTRY, 1996, Vol.1, pp.11-17
(97124)
TI: Strength of hydrogen bonds in alpha helices
AU: Arora_N, Jayaram_B
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.9, pp.1245-1252
(97125)
TI: Development and validation of force-field parameters for molecular
simulations of peptides and proteins containing open-shell residues
AU: Barone_V, Capecchi_G, Brunel_Y, Andries_MLD, Subra_R
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.14, pp.1720-1728
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TI: Hydrogen bonding interactions between glutamine and asparagine
in alpha-helical peptides
AU: Stapley_BJ, Doig_AJ
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.272, No.3, pp.465-473
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TI: Conformational analysis of homochiral and heterochiral diprolines as
beta-turn-forming peptidomimetics: Unsubstituted and substituted
models
AU: Baures_PW, Ojala_WH, Gleason_WB, Johnson_RL
JN: JOURNAL OF PEPTIDE RESEARCH, 1997, Vol.50, No.1, pp.1-13
(97128)
TI: IMPROVING THE QUALITY OF NMR AND CRYSTALLOGRAPHIC PROTEIN STRUCTURES
BY MEANS OF A CONFORMATIONAL DATABASE POTENTIAL DERIVED FROM
STRUCTURE DATABASES
AU: KUSZEWSKI_J, GRONENBORN_AM, CLORE_GM
JN: PROTEIN SCIENCE, 1996, Vol.5, No.6, pp.1067-1080
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TI: Discrete representations of the protein C-alpha chain
AU: delaCruz_XF, Mahoney_MW, Lee_B
JN: FOLDING & DESIGN, 1997, Vol.2, No.4, pp.223-234
(97130)
TI: Local interactions of aromatic residues in short peptides in aqueous
solution: a combined database and energetic analysis
AU: Nardi_F, Worth_GA, Wade_RC
JN: FOLDING & DESIGN, 1997, Vol.2, No.4, pp.S62-S68
(97131)
TI: High-pressure krypton gas and statistical heavy-atom refinement: A
successful combination of tools for macromolecular structure
determination
AU: Schiltz_M, Shepard_W, Fourme_R, Prange_T, DeLaFortelle_E, Bricogne_G
JN: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1997,
Vol.53, No.Pt1, pp.78-92
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TI: The future of protein secondary structure prediction accuracy
AU: Frishman_D, Argos_P
JN: FOLDING & DESIGN, 1997, Vol.2, No.3, pp.159-162
(97133)
TI: Direct evaluation of thermal fluctuations in proteins using a single-
parameter harmonic potential
AU: Bahar_I, Atilgan_AR, Erman_B
JN: FOLDING & DESIGN, 1997, Vol.2, No.3, pp.173-181
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TI: Solution Structure of the First Three Zinc Fingers of TFIIIA
Bound to the Cognate DNA Sequence: Determinants of Affinity
and Sequence Specificity
AU: Wuttke_DS, Foster_MP, Case_DA, Gottesfeld_JM, Wright_PE
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.273, No.1, pp.183-206
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TI: Understanding alpha-amino acid chemistry from x-ray diffraction
structures
AU: Toniolo_C, Crisma_M, Formaggio_F
JN: BIOPOLYMERS, 1996, Vol.40, No.6, pp.627-651
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TI: Phi/psi-chology: Ramachandran revisited
AU: Kleywegt_GJ, Jones_TA
JN: STRUCTURE, 1996, Vol.4, No.12, pp.1395-1400
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TI: STRUCTURAL-ENGINEERING OF THE HIV-1 PROTEASE MOLECULE WITH A BETA-
TURN MIMIC OF FIXED GEOMETRY
AU: BACA_M, ALEWOOD_PF, KENT_SBH
JN: PROTEIN SCIENCE, 1993, Vol.2, No.7, pp.1085-1091
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TI: SYNTHESIS OF A BICYCLIC DIPEPTIDE WITH THE SHAPE OF BETA-TURN CENTRAL
PART
AU: NAGAI_U, SATO_K
JN: TETRAHEDRON LETTERS, 1985, Vol.26, No.5, pp.647-650
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TI: ECONOMY IN PROTEIN DESIGN - EVOLUTION OF A METAL-INDEPENDENT BETA-
BETA-ALPHA MOTIF BASED ON THE ZINC-FINGER DOMAINS
AU: STRUTHERS_MD, CHENG_RP, IMPERIALI_B
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, Vol.118, No.13,
pp.3073-3081
(97140)
TI: COCRYSTAL STRUCTURE OF YY1 BOUND TO THE ADENOASSOCIATED VIRUS P5
INITIATOR
AU: HOUBAVIY_HB, USHEVA_A, SHENK_T, BURLEY_SK
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES
OF AMERICA, 1996, Vol.93, No.24, pp.13577-13582
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TI: A NEW ANISOTROPIC FORCE-YIELD FOR THE HYDROGEN-BOND - STUDY OF WATER
CLUSTERS
AU: MASELLA_M, LEFOUR_JM, FLAMENT_JP
JN: BULLETIN DE LA SOCIETE CHIMIQUE DE FRANCE, 1995, Vol.132, No.2,
pp.224-232
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TI: A new anisotropic force field for hydrogen bonding .3. A simple
solvation model for ethane-1,2-diol
AU: Masella_M, Flament_JP
JN: BULLETIN DE LA SOCIETE CHIMIQUE DE FRANCE, 1997, Vol.134, No.5,
pp.439-449
(97143)
TI: Residue-residue mean-force potentials for protein structure
recognition
AU: Reva_BA, Finkelstein_AV, Sanner_MF, Olson_AJ
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.8, pp.865-876
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TI: Modelling protein unfolding: hen egg-white lysozyme
AU: Williams_MA, Thornton_JM, Goodfellow_JM
JN: PROTEIN ENGINEERING 1997 Vol.10 No.8, pp.895-903
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TI: Basis set modeling for molecular calculations using effective core
potential
AU: Giordan_M, Custodio_R
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.15, pp.1918-1929
(97146)
TI: Representing protein and peptide structures with parallel-coordinates
AU: Becker_OM
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.15, pp.1893-1902
(97147)
TI: Redefining the atom
AU: Raos_N
JN: CHEMISTRY IN BRITAIN, 1997, Vol.33, No.2, pp.31-32
(97148)
TI: The cation-pi interaction
AU: Ma_JC, Dougherty_DA
JN: CHEMICAL REVIEWS, 1997, Vol.97, No.5, pp.1303-1324
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TI: AQUARIUS2 - KNOWLEDGE-BASED MODELING OF SOLVENT SITES AROUND PROTEINS
AU: PITT_WR, MURRAYRUST_J, GOODFELLOW_JM
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1993, Vol.14, No.9, pp.1007-1018
(9801)
TI: De novo protein design: Towards fully automated sequence selection
AU: Dahiyat_BI, Sarisky_CA, Mayo_SL
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.273, No.4, pp.789-796
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TI: NEW METHODS FOR THE ANALYSIS OF THE PROTEIN SOLVENT INTERFACE
AU: GOODFELLOW_JM, PITT_WR, SMART_OS, WILLIAMS_MA
JN: COMPUTER PHYSICS COMMUNICATIONS, 1995, Vol.91, No.1-3, pp.321-329
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TI: Density-functional methods for the study of the ground-state
vibrations of the guanidinium ion
AU: Magalhes_AL, Gomes_JANF
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1997, Vol.61, No.4,
pp.725-739
(9804)
TI: RATIONAL DESIGN OF POTENT SIALIDASE-BASED INHIBITORS OF INFLUENZA-
VIRUS REPLICATION
AU: VONITZSTEIN_M, WU_WY, KOK_GB, PEGG_MS, DYASON_JC, JIN_B, PHAN_TV,
SMYTHE_ML, WHITE_HF, OLIVER_SW, COLMAN_PM, VARGHESE_JN, RYAN_DM,
WOODS_JM, BETHELL_RC, HOTHAM_VJ, CAMERON_JM, PENN_CR
JN: NATURE, 1993, Vol.363, No.6428, pp.418-423
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TI: How protein chemists learned about the hydrophobic factor
AU: Tanford_C
JN: PROTEIN SCIENCE, 1997, Vol.6, No.6, pp.1358-1366
(9806)
TI: DETAILS OF THE ACYL-ENZYME INTERMEDIATE AND THE OXYANION HOLE IN
SERINE-PROTEASE CATALYSIS
AU: WHITING_AK, PETICOLAS_WL
JN: BIOCHEMISTRY, 1994, Vol.33, No.2, pp.552-561
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TI: The partial charge of the nitrogen atom in peptide bonds
AU: MilnerWhite_EJ
JN: PROTEIN SCIENCE, 1997, Vol.6, No.11, pp.2477-2482
(9808)
TI: Ideal architecture of residue packing and its observation in
protein structures
AU: Raghunathan_G, Jernigan_RL
JN: PROTEIN SCIENCE, 1997, Vol.6, No.10, pp.2072-2083
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TI: WHY DO PROTEIN ARCHITECTURES HAVE BOLTZMANN-LIKE STATISTICS
AU: FINKELSTEIN_AV, BADRETDINOV_AY, GUTIN_AM
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1995, Vol.23, No.2, pp.142-150
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TI: PERFECT TEMPERATURE FOR PROTEIN-STRUCTURE PREDICTION AND FOLDING
AU: FINKELSTEIN_AV, GUTIN_AM, BADRETDINOV_AY
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1995, Vol.23, No.2, pp.151-162
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TI: Validation of protein models from C-alpha coordinates alone
AU: Kleywegt_GJ
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.273, No.2, pp.371-376
(9812)
TI: Organic chemistry - Polymer folds just like a protein
AU: Pennisi_E
JN: SCIENCE, 1997, Vol.277, No.5333, p.1764
(9813)
TI: Prebiotic evolution: Selecting for homochirality before RNA
AU: Schwartz_AW
JN: CURRENT BIOLOGY, 1997, Vol.7, No.8, pp.R477-R479
(9814)
TI: PREDICTION OF PROTEIN COMPLEXES USING EMPIRICAL FREE-ENERGY FUNCTIONS
AU: WENG_ZP, VAJDA_S, DELISI_C
JN: PROTEIN SCIENCE, 1996, Vol.5, No.4, pp.614-626
(9815)
TI: Fourier-filtered van der Waals contact surfaces: accurate
ligand shapes from protein structures
AU: Friedman_JM
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.8, pp.851-863
(9816)
TI: Protein clefts in molecular recognition and function
AU: Laskowski_RA, Luscombe_NM, Swindells_MB, Thornton_JM
JN: PROTEIN SCIENCE, 1996, Vol.5, No.12, pp.2438-2452
(9817)
TI: QUALITY-CONTROL OF PROTEIN MODELS - DIRECTIONAL ATOMIC CONTACT
ANALYSIS
AU: VRIEND_G, SANDER_C
JN: JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1993, Vol.26, No.Pt1, pp.47-60
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TI: Equilibrium geometries and electronic structure of iron-porphyrin
complexes: A density functional study
AU: Rovira_C, Kunc_K, Hutter_J, Ballone_P, Parrinello_M
JN: JOURNAL OF PHYSICAL CHEMISTRY A, 1997, Vol.101, No.47, pp.8914-892
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TI: DENSITY-FUNCTIONAL THEORY PREDICTION OF THE 2ND-ORDER
HYPERPOLARIZABILITY OF METALLOPORPHINES
AU: MATSUZAWA_N, ATA_M, DIXON_DA
JN: JOURNAL OF PHYSICAL CHEMISTRY, 1995, Vol.99, No.19, pp.7698-7706
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TI: Empirical potentials and functions for protein folding and
binding
AU: Vajda_S, Sippl_M, Novotny_J
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1997, Vol.7, No.2,
pp.222-228
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TI: Helmholtz free energies of atom pair interactions in proteins
AU: Sippl_MJ, Ortner_M, Jaritz_M, Lackner_P, Flockner_H
JN: FOLDING & DESIGN, 1996, Vol.1, No.4, pp.289-298
(9822)
TI: THE HYDROGEN-BOND C-H DONOR AND PI-ACCEPTOR CHARACTERISTICS OF 3-
MEMBERED RINGS
AU: ALLEN_FH, LOMMERSE_JPM, HOY_VJ, HOWARD_JAK, DESIRAJU_GR
JN: ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 1996, Vol.52,
No.Pt4, pp.734-745
(9823)
TI: Chemistry - Mimicking an enzyme in look and deed
AU: Service_RF
JN: SCIENCE, 1998, Vol.279, No.5350, pp.479-480
(9824)
TI: Catalytic galactose oxidase models: Biomimetic Cu(II)-phenoxyl-
radical reactivity
AU: Wang_YD, DuBois_JL, Hedman_B, Hodgson_KO, Stack_TDP
JN: SCIENCE, 1998, Vol.279, No.5350, pp.537-540
(9825)
TI: Solvent effects on a Diels-Alder reaction involving a cationic diene:
Consequences of the absence of hydrogen-bond interactions for
accelerations in aqueous media
AU: vanderWel_GK, Wijnen_JW, Engberts_JBFN
JN: JOURNAL OF ORGANIC CHEMISTRY, 1996, Vol.61, No.25, pp.9001-9005
(9826)
TI: Water molecules hydrogen bonding to aromatic acceptors of amino acids:
the structure of Tyr-Tyr-Phe dihydrate and a crystallographic database
study on peptides
AU: Steiner_T, Schreurs_AMM, Kanters_JA, Kroon_J
JN: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998,
Vol.54, No.Pt1, pp.25-31
(9827)
TI: How do potentials derived from structural databases relate to
''true'' potentials?
AU: Zhang_L, Skolnick_J
JN: PROTEIN SCIENCE, 1998, Vol.7, No.1, pp.112-122
(9828)
TI: GENETICS AND SPECIATION
AU: COYNE_JA
JN: NATURE, 1992, Vol.355, No.6360, pp.511-515
(9829)
TI: GENETIC-DIVERGENCE, SPECIATION AND MORPHOLOGICAL STASIS IN A LINEAGE
OF AFRICAN CICHLID FISHES
AU: STURMBAUER_C, MEYER_A
JN: NATURE, 1992, Vol.358, No.6387, pp.578-581
(9830)
TI: Zinc fingers are sticking together
AU: Mackay_JP, Crossley_M
JN: TRENDS IN BIOCHEMICAL SCIENCES, 1998, Vol.23, No.1, pp.1-4
(9831)
TI: Are changes in integrin affinity and conformation
overemphasized?
AU: Bazzoni_G, Hemler_ME
JN: TRENDS IN BIOCHEMICAL SCIENCES, 1998, Vol.23, No.1, pp.30-34
(9832)
TI: An atlas of protein topology cartoons available on the World-
Wide Web
AU: Westhead_DR, Hatton_DC, Thornton_JM
JN: TRENDS IN BIOCHEMICAL SCIENCES, 1998, Vol.23, No.1, pp.35-36
(9833)
TI: Protein distance constraints predicted by neural networks and
probability density functions
AU: Lund_O, Frimand_K, Gorodkin_J, Bohr_H, Bohr_J, Hansen_J,
Brunak_S
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.11, pp.1241-1248
(9834)
TI: A fast estimate of electrostatic group contributions to
the free energy of protein-inhibitor binding
AU: Muegge_I, Tao_H, Warshel_A
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.12, pp.1363-1372
(9835)
TI: Is there a Mobius band in closed protein beta-sheets?
AU: Liu_W
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.12, pp.1357-1361
(9836)
TI: Hydrogen bonds and salt bridges across protein-protein
interfaces
AU: Xu_D, Tsai_CJ, Nussinov_R
JN: PROTEIN ENGINEERING, 1997, Vol.10, No.9, pp.999-1012
(9837)
TI: Evolution of model proteins on a foldability landscape
AU: Govindarajan_S, Goldstein_RA
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.29, No.4,
pp.461-466
(9838)
TI: Highly constrained multiple-copy refinement of protein crystal
structures
AU: Pellegrini_M, GronbechJensen_N, Kelly_JA, Pfluegl_GMU,
Yeates_TO
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.29, No.4,
pp.426-432
(9839)
TI: Short-range conformational energies, secondary structure
propensities, and recognition of correct sequence-structure
matches
AU: Bahar_I, Kaplan_M, Jernigan_RL
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.29, No.3,
pp.292-308
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TI: A report on the 1997 John Hopkins protein folding meeting
AU: Wehrle_JP
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.29, No.3,
pp.259-263
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TI: Calculations on the low energy conformers of N-acetyl-O-alanyl-
D-alanine
AU: Frau_J, Donoso_J, Munoz_F, Blanco_FG
JN: BIOPOLYMERS, 1998, Vol.45, No.2, pp.119-133
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TI: An experimental Ramachandran plot for retropeptide derivatives:
Conformational features of derivatives of GEM-diamino and
malonyl amino acids
AU: Puiggali_J, Subirana_JA
JN: BIOPOLYMERS, 1998, Vol.45, No.2, pp.149-155
(9843)
TI: Hydrogen bonding properties of oxygen and nitrogen acceptors in
aromatic heterocycles
AU: Nobeli_I, Price_SL, Lommerse_JPM, Taylor_R
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No.16, pp.2060-2074
(9844)
TI: Conformational interconversions in peptide -turns: Discrimination
between enantiomeric conformations by chiral perturbation
AU: Raghothama_S, Chaddha_M, Banumathi_S, Ravikumar_K, Velmurugan_D,
Balaram_P
JN: BIOPOLYMERS, 1998, Vol.45, No.3, pp.191-202
(9845)
TI: A computational analysis of the unique protein-induced tight turn
that results in posttranslational chromophore formation in green
fluorescent protein
AU: Branchini_BR, Nemser_AR, Zimmer_M
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, Vol.120, No.1, pp.1-6
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TI: A charge-transfer complex of xenon and difluorovinylidene
AU: Kotting_C, Sander_W, Breidung_J, Thiel_W, Senzlober_M, Burger_H
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, Vol.120, No.1,
pp.219-220
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TI: Side chains affect electron tunneling rates across amino acids
AU: Tsai_TC, Chang_IJ
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, Vol.120, No.1,
pp.227-228
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TI: A de novo design probe of a dopamine receptor ligand based on a
theoretical approach
AU: Baginski_M, Claudi_F, Giorgioni_G, Fontenla_JA, Rosa_E, Cardellini_M
JN: BIOORGANIC CHEMISTRY, 1996, Vol.24, No.4, pp.358-375
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TI: SOLUTION STRUCTURE OF A PARALLEL LEFT-HANDED DOUBLE-HELICAL
GRAMICIDIN-A DETERMINED BY 2D H-1-NMR
AU: CHEN_Y, TUCKER_A, WALLACE_BA
JN: JOURNAL OF MOLECULAR BIOLOGY, 1996, Vol.264, No.4, pp.757-769
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TI: Topological analysis of the experimental electron densities
of amino acids. 1. DL-aspartic acid at 20K
AU: Flaig_R, Koritsanszky_T, Zobel_D, Luger_P
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, Vol.120,
pp.2227-2238
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TI: THE CRYSTAL-STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE
FACTOR REFINED TO 1.7 ANGSTROM RESOLUTION
AU: MULLER_YA, ULTSCH_MH, DEVOS_AM
JN: JOURNAL OF MOLECULAR BIOLOGY, 1996, Vol.256, No.1, pp.144-159
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TI: THE HISTORY AND EVOLUTION OF GAUSSIAN BASIS SETS
AU: SHAVITT_I
JN: ISRAEL JOURNAL OF CHEMISTRY, 1993, Vol.33,pp.357-367
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TI: Contribution of water molecules in the interior of a protein to
the conformational stability
AU: Takano_K, Funahashi_J, Yamagata_Y, Fujii_S, Yutani_K
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.274, No.1, pp.132-142
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TI: Structural characterization of the myoglobin active site using
infrared crystallography
AU: Sage_JT, Jee_W
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.274, No.1, pp.21-26
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TI: The entropy cost of protein association
AU: Tamura_A, Privalov_PL
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.273, No.5, pp.1048-1060
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TI: Electrostatic and non-electrostatic contributions to the
binding free energies of anthracycline antibiotics to DNA
AU: Baginski_M, Fogolari_F, Briggs_JM
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.274, No.2, pp.253-267
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TI: Role of beta-turn residues in beta-hairpin formation and
stability in designed peptides
AU: RamirezAlvarado_M, Blanco_FJ, Niemann_H, Serrano_L
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.273, No.4, pp.898-912
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TI: Assessing protein structures with a non-local atomic
interaction energy
AU: Melo_F, Feytmans_E
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.277, No.5, pp.1141-1152
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TI: Recognition of errors in three-dimensional structures
of proteins
AU: Sippl_MJ
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1993, Vol.17, No.3,
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TI: Are knowledge-based potentials derived from protein structure
sets discriminative with respect to amino acid types?
AU: Sunyaev_SR, Eisenhaber_F, Argos_P, Kuznetsov_EN, Tumanyan_VG
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.31, No.3,
pp.225-246
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TI: Extracting contact energies from protein structures: A study
using a simplified model
AU: Zhang_C
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.31, No.3,
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TI: Interaction potentials for protein folding
AU: Seno_F, Maritan_A, Banavar_JR
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.30, No.3,
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TI: Improved protein free energy calculation by more accurate
treatment of nonbonded energy: Application to chymotrypsin
inhibitor 2, V57A
AU: Sugita_Y, Kitao_A
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.30, No.4,
pp.388-400
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TI: Does the methyl group form a hydrogen bond? Ab initio
post- Hartree-Fock
study on ethane-hydrogen cyanide complex
AU: Komasa_J, Szalewicz_K, Leszczynski_J
JN: CHEMICAL PHYSICS LETTERS, 1998, Vol.285, No.5-6, pp.449-454
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TI: CH/pi interactions as demonstrated in the crystal structure of
guanine-nucleotide binding proteins, Src homology-2 domains and human
growth hormone in complex with their specific ligands
AU: Umezawa_Y, Nishio_M
JN: BIOORGANIC & MEDICINAL CHEMISTRY, 1998, Vol.6, No.4, pp.493-504
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TI: CH/pi interaction in the crystal structure of organic compounds.
A database study.
AU: Umezawa_Y, Tsuboyama_S, Honda_K, Uzawa_J, Nishio_M
JN: BULL. CHIM. SOC. JPN., 1998, Vol.71, pp.1207-1213
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TI: Apologia.
AU: Dahiyat_BI, Sarisky_CA, Mayo_SL
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.279, No.4, p.1023
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TI: Prediction of protein hydration sites from sequence by
modular neural networks
AU: Ehrlich_L, Reczko_M, Bohr_H, Wade_RC
JN: PROTEIN ENGINEERING, 1998, Vol.11, No.1, pp.11-19
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TI: High-resolution structures of variant Zif268-DNA complexes:
Implications for understanding zinc finger-DNA recognition
AU: ElrodErickson_M, Benson_TE, Pabo_CO
JN: STRUCTURE, 1998, Vol.6 No.4, pp.451-464
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TI: Computation of electrostatic complements to proteins: A case of
charge stabilized binding
AU: Chong_LT, Dempster_SE, Hendsch_ZS, Lee_LP, Tidor_B
JN: PROTEIN SCIENCE, 1998, Vol.7, No.1, pp.206-210
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TI: What should the Z-score of native protein structures be?
AU: Zhang_L, Skolnick_J
JN: PROTEIN SCIENCE, 1998, Vol.7, No.5, pp.1201-1207
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TI: An all-atom distance-dependent conditional probability
discriminatory function for protein structure prediction
AU: Samudrala_R, Moult_J
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.275, No.5, pp.895-916
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TI: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures
AU: Wilson_KS, Butterworth_S, Dauter_Z, Lamzin_VS, Walsh_M, Wodak_S,
Pontius_J, Richelle_J, Vaguine_A, Sander_C, Hooft_RWW, Vriend_G,
Thornton_JM, Laskowski_RA, MacArthur_MW, Dodson_EJ, Murshudov_G,
Oldfield_TJ, Kaptein_R, Rullmann_JAC
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.276, No.2, pp.417-436
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TI: Density functional studies on herpes simplex virus type 1
thymidine kinase-substrate interactions: The role of Tyr-172
and Met-128 in thymine fixation
AU: Alber_F, Kuonen_O, Scapozza_L, Folkers_G, Carloni_P
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.31, No.4,
pp.453-459
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TI: Electrostatics, allostery, and activity of the yeast chorismate
mutase
AU: Lin_SL, Xu_D, Li_AJ, Nussinov_R
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.31, No.4,
pp.445-452
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TI: The role played by environmental residues on sidechain
torsional angles within homologous families of proteins: A new
method of sidechain modeling
AU: Ogata_K, Umeyama_H
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.31, No.4,
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TI: Effect of electrostatic interactions in recognition of acetylcholine
by acetylcholinesterase
AU: Linaras_CE, Singh_K, Kristol_D, Ritter_AB
JN: THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, 1998, Vol.425, No.1-2,
pp.81-85
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TI: RNA-directed amino acid homochirality
AU: Bailey_JM
JN: FASEB JOURNAL, 1998, Vol.12, No.6, pp.503-507
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TI: ACCURATE BOND AND ANGLE PARAMETERS FOR X-RAY PROTEIN-STRUCTURE
REFINEMENT
AU: ENGH_RA, HUBER_R
JN: ACTA CRYSTALLOGRAPHICA SECTION A-FUNDAMENTALS OF CRYSTALLOGRAPHY,
1991, Vol.47, No.JUL, pp.392-400
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TI: On the potential role of the amino nitrogen atom as a hydrogen
bond acceptor in macromolecules
AU: Luisi_B, Orozco_M, Sponer_J, Luque_FJ, Shakked_Z
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.279, No.5, pp.1123-1136
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TI: Detection of protein three-dimensional side-chain patterns: New
examples of convergent evolution
AU: Russell_RB
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.279, No.5, pp.1211-1227
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TI: Reengineering immunoglobulin domain interactions by introduction of
charged residues
AU: Raffen_R, Stevens_PW, Boogaard_C, Schiffer_M, Stevens_FJ
JN: PROTEIN ENGINEERING, 1998, Vol.11, No.4, pp.303-309
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TI: Estimates of relative binding free energies for HIV protease
inhibitors using different levels of approximations
AU: Lee_CY, Yang_PK, Tzou_WS, Hwang_MJ
JN: PROTEIN ENGINEERING, 1998, Vol.11, No.6, pp.429-437
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TI: Leading scientists still reject God
AU: Larson_EJ, Witham_L
JN: NATURE, 1998, Vol.394, No.6691, p.313
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TI: Other worlds: The search for life in the Universe - Lemonick,MD
AU: Hughes_DW
JN: NATURE, 1998, Vol.394, No.6691, p.336
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TI: On the stabilization of natural L-enantiomers of alpha-amino
acids via parity-violating effects
AU: Zanasi_R, Lazzeretti_P
JN: CHEMICAL PHYSICS LETTERS, 1998, Vol.286, pp. 240-242
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TI: Protein folding - Matching speed and locality
AU: Chan_HS
JN: NATURE, 1998, Vol.392, No.6678, pp.761-763
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TI: After contact: The human response to extraterrestrial life -
Harrison,AA
AU: Morrison_P
JN: NATURE, 1998, Vol.391, No.6666, p.451
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TI: Protein structure - Topological nuts and bolts
AU: Nash_HA
JN: SCIENCE, 1998, Vol.279, No.5356, pp.1490-1491
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TI: Reaction dynamics
AU: Uppenbrink_J
JN: SCIENCE, 1998, Vol.279, No.5358, p.1831
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TI: Quantum theory of chemical reaction dynamics
AU: Clary_DC
JN: SCIENCE, 1998, Vol.279, No.5358, pp.1879-1882
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TI: Accurate experimental electronic properties of DL-proline monohydrate
obtained within 1 day
AU: Koritsanszky_T, Flaig_R, Zobel_D, Krane_HG, Morgenroth_W, Luger_P
JN: SCIENCE, 1998, Vol.279, No.5349, pp.356-358
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TI: Rite of initiation
JN: NATURE STRUCURAL BIOLOGY, 1997, Vol.4, No.1, pp1-2
AU: Editorial
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TI: Who was Angstrom?
JN: NATURE STRUCTURAL BIOLOGY, 1998, Vol.5, No.3, p.177
AU: Smith_TL
(9895)
TI: Quantum mechanical calculations on biological systems
AU: Friesner_RA, Beachy_MD
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1998, Vol.8, No.2,
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TI: Theory of biomolecular recognition
AU: McCammon_JA
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1998, Vol.8, No.2,
pp.245-249
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TI: Electrostatic effects in macromolecules: fundamental concepts
and practical modeling
AU: Warshel_A, Papazyan_A
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1998, Vol.8, No.2,
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TI: Theory and simulation - Overview
AU: Goodfellow_JM, Levy_RM
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1998, Vol.8, No.2,
pp.209-210
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TI: Protein hydration density: theory, simulations and
crystallography
AU: Pettitt_BM, Makarov_VA, Andrews_BK
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1998, Vol.8, No.2,
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TI: H-H model potential for exchange-repulsion energy of methane dimer
AU: Fraschini_E, Stone_AJ
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.8, pp.847-857
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TI: Directional hydrogen bonding in the MM3 force field: II
AU: Lii_JH, Allinger_NL
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.9, pp.1001-1016
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TI: Averaged electron densities for averaged conformations
AU: Mezey_PG
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.12, pp.1337-1344
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TI: Low-barrier hydrogen bonds: ab initio and DFT investigation
AU: Kumar_GA, Pan_Y, Smallwood_CJ, McAllister_MA
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.12, pp.1345-1352
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TI: Crystal structure predictions for acetic acid
AU: Mooij_WTM, vanEijck_BP, Price_SL, Verwer_P, Kroon_J
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.4, pp.459-474
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TI: Combined ab initio empirical approach for optimization of Lennard-
Jones parameters
AU: Yin_DX, Mackerell_AD
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.3, pp.334-348
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TI: Hydration of an alpha-helical peptide: comparison of theory and
molecular dynamics simulation
AU: Garcia_AE, Hummer_G, Soumpasis_DM
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.27, No.4,
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TI: Ordered water in macromolecular structure
AU: Karplus_PA, Faerman_C
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1994, Vol.4, No.5,
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TI: Docking enzyme-inhibitor complexes using a preference-based
free-energy surface
AU: Wallqvist_A, Covell_DG
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1996, Vol.25, No.4,
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TI: Empirical free energy calculations: a blind test and further
improvements to the method
AU: Novotny_J, Bruccoleri_RE, Davis_M, Sharp_KA
JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.268, pp.401-411
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TI: Calculation of the free energy of association for protein
complexes
AU: Horton_N, Lewis_M
JN: PROTEIN SCIENCE, 1992, Vol.1, No.1, pp.169-181
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TI: A stable methyl phosphane oxide lithium amide complex: A structural
and MO calculational investigation of the mechanism of proton
abstraction by alkali metal reagents
AU: Armstrong_DR, Davidson_MG, Davies_RP, Mitchell_HJ, Oakley_RM,
Raithby_PR, Snaith_R, Warren_S
JN: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION IN ENGLISH, 1996, Vol.35,
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TI: Modelling protein docking using shape complementarity, electrostatics
and biochemical information
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JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.272, No.1, pp.106-120
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TI: FGF BINDING AND FGF RECEPTOR ACTIVATION BY SYNTHETIC HEPARAN-DERIVED
DISACCHARIDES AND TRISACCHARIDES
AU: ORNITZ_DM, HERR_AB, NILSSON_M, WESTMAN_J, SVAHN_CM, WAKSMAN_G
JN: SCIENCE, 1995, Vol.268, No.5209, pp.432-436
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TI: THE DEVELOPMENT OF A SIMPLE EMPIRICAL SCORING FUNCTION TO ESTIMATE
THE BINDING CONSTANT FOR A PROTEIN LIGAND COMPLEX OF KNOWN 3-
DIMENSIONAL STRUCTURE
AU: BOHM_HJ
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, Vol.8, No.3,
pp.243-256
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TI: SHAPE INFORMATION FROM A CRITICAL-POINT ANALYSIS OF CALCULATED
ELECTRON-DENSITY MAPS - APPLICATION TO DNA-DRUG SYSTEMS
AU: LEHERTE_L, ALLEN_FH
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, Vol.8, No.3,
pp.257-272
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TI: Heparin structure and interactions with basic fibroblast growth
factor
AU: Faham_S, Hileman_RE, Fromm_JR, Linhardt_RJ, Rees_DC
JN: SCIENCE, 1996, Vol.271, No.5252, pp.1116-1120
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TI: A re-estimation for the total numbers of protein folds and
superfamilies
AU: Wang_ZX
JN: PROTEIN ENGINEERING, 1998, Vol.11, No.8, pp.621-626
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TI: Main-chain conformational features at different conformations
of the side-chains in proteins
AU: Chakrabarti_P, Pal_D
JN: PROTEIN ENGINEERING, 1998, Vol.11, No.8, pp.631-647
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TI: Accuracy of electronic wave functions in quantum Monte Carlo: The
effect of high-order correlations
AU: Huang_CJ, Umrigar_CJ, Nightingale_MP
JN: JOURNAL OF CHEMICAL PHYSICS, 1997, Vol.107, No.8, pp.3007-3013
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TI: Local control of peptide conformation: Stabilization of cis
proline peptide bonds by aromatic proline interactions
AU: Wu_WJ, Raleigh_DP
JN: BIOPOLYMERS, 1998, Vol.45, No.5, pp.381-394
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TI: Reconstructing the protein-water interface
AU: Makarov_VA, Andrews_BK, Pettitt_BM
JN: BIOPOLYMERS, 1998, Vol.45, No.7, pp.469-478
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TI: Stick-slip phase transitions in confined solidlike films from an
equilibrium perspective
AU: Bordarier_P, Schoen_M, Fuchs_AH
JN: PHYSICAL REVIEW E, 1998, Vol.57, No.2 PtA, pp.1621-1635
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TI: Rheology of model confined ultrathin fluid films .1. Statistical
mechanics of the surface force apparatus experiments
AU: Bordarier_P, Rousseau_B, Fuchs_AH
JN: JOURNAL OF CHEMICAL PHYSICS, 1997, Vol.106, No.17, pp.7295-7302
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TI: Temperature and density dependence of the self-diffusion coefficient
and Mori coefficients of Lennard-Jones fluids by molecular dynamics
simulation
AU: Nuevo_MJ, Morales_JJ, Heyes_DM
JN: PHYSICAL REVIEW E, 1997, Vol.55, No.4, pp.4217-4224
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TI: Competitive solvation of K+ by benzene and water: Cation-pi
interactions and pi-hydrogen bonds
AU: Cabarcos_OM, Weinheimer_CJ, Lisy_JM
JN: JOURNAL OF CHEMICAL PHYSICS, 1998, Vol.108, No.13, pp.5151-5154
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TI: X-ray crystal structure of a dipeptide-chymotrypsin complex in an
inhibitory interaction
AU: Kashima_A, Inoue_Y, Sugio_S, Maeda_I, Nose_T, Shimohigashi_Y
JN: EUROPEAN JOURNAL OF BIOCHEMISTRY, 1998, Vol.255, No.1, pp.12-23
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TI: Salt bridge interactions: Stability of the ionic and neutral
complexes in the gas phase, in solution, and in proteins
AU: Barril_X, Aleman_C, Orozco_M, Luque_FJ
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.32, No.1, pp.67-
79
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TI: A mean field model of ligand protein interactions: Implications for
the structural assessment of human immunodeficiency virus type 1
protease complexes and receptor-specific binding
AU: Verkhivker_GM, Rejto_PA
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES
OF AMERICA, 1996, Vol.93, No.1, pp.60-64
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TI: Mean field analysis of FKBP12 complexes with FK506 and rapamycin:
Implications for a role of crystallographic water molecules in
molecular recognition and specificity
AU: Rejto_PA, Verkhivker_GM
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.28, No.3, pp.313-
324
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TI: The three-dimensional structure of shikimate kinase
AU: Krell_T, Coggins_JR, Lapthorn_AJ
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.278, No.5, pp.983-997
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TI: The mechanism of the elongation and branching reaction of poly(ADP-
ribose) polymerase as derived from crystal structures and mutagenesis
AU: Ruf_A, Rolli_V, deMurcia_G, Schulz_GE
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.278, No.1, pp.57-65
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TI: Correlation of the enzyme activities of Bacillus stearothermophilus
lactate dehydrogenase on three substrates with the results of
molecular dynamics energy minimization conformational searching
AU: Dafforn_TR, Badcoe_IG, Sessions_RB, ElHawrani_AS, Holbrook_JJ
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1997, Vol.29, No.2, pp.228-
239
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TI: SMoG: De novo design method based on simple, fast, and accurate free
energy estimates .2. Case studies in molecular design
AU: DeWitte_RS, Ishchenko_AV, Shakhnovich_EI
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1997, Vol.119, No.20,
pp.4608-4617
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TI: A new method for predicting binding free energy between
receptor and ligand
AU: Takamatsu_Y, Itai_A
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.33, No.1,
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TI: Analytical shape computation of macromolecules: I. Molecular
area and volume through alpha shape
AU: Liang_J, Edelsbrunner_H, Fu_P, Sudhakar_PV, Subramaniam_S
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.33, No.1,
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TI: Analytical shape computation of macromolecules: II.
Inaccessible cavities in proteins
AU: Liang_J, Edelsbrunner_H, Fu_P, Sudhakar_PV, Subramaniam_S
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1998, Vol.33, No.1,
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TI: Electrostatic contributions to the stability of halophilic
proteins
AU: Elcock_AH, McCammon_JA
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.280, No.4, pp.731-748
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TI: QUANTUM CRYSTALLOGRAPHY AND THE USE OF KERNEL PROJECTOR MATRICES
AU: MASSA_L, HUANG_L, KARLE_J
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1995, No.S29, pp.371-384
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TI: THE NATURE AND GEOMETRY OF INTERMOLECULAR INTERACTIONS BETWEEN
HALOGENS AND OXYGEN OR NITROGEN
AU: LOMMERSE_JPM, STONE_AJ, TAYLOR_R, ALLEN_FH
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, Vol.118, No.13,
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TI: SMoG: de Novo design method based on simple, fast, and accurate free
energy estimates .1. Methodology and supporting evidence
AU: DeWitte_RS, Shakhnovich_EI
JN: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, Vol.118, No.47,
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TI: The chemical Hamiltonian approach for treating the BSSE problem of
intermolecular interactions
AU: Mayer_I
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.70, No.1,
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TI: Density functional theory in relation to X-ray and neutron scattering
experiments
AU: March_NH
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.69, No.4,
pp.551-557
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TI: Calculation of ligand binding free energies from molecular dynamics
simulations
AU: Marelius_J, Hansson_T, Aqvist_J
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.69, No.1,
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TI: Ab initio and density functional theory studies of the catalytic
mechanism for ester hydrolysis in serine hydrolases
AU: Hu_CH, Brinck_T, Hult_K
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.69, No.1,
pp.89-103
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TI: Ab initio study of the structure of isocytosine-cytosine standard
Watson-Crick base pairs in the gas phase and in water
AU: Zhanpeisov_NU, Leszczynski_J
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.69, No.1,
pp.37-47
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TI: Life's other secret: The new mathematics of the living world -
Stewart,I
AU: Bray_D
JN: NATURE, 1998, Vol.394, No.6692, pp.436-437
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TI: Three-dimensional domain duplication, swapping and stealing
AU: Heringa_J, Taylor_WR
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1997, Vol.7, No.3,
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TI: Progress in protein structure prediction
AU: Jones_DT
JN: CURRENT OPINION IN STRUCTURAL BIOLOGY, 1997, Vol.7, No.3,
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TI: Not your average density
AU: Kleywegt_GJ, Read_RJ
JN: STRUCTURE, 1997, Vol.5, No.12, pp.1557-1569
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TI: Solution structure of the heparin-binding domain of vascular
endothelial growth factor
AU: Fairbrother_WJ, Champe_MA, Christinger_HW, Keyt_BA,
Starovasnik_MA
JN: STRUCTURE, 1998, Vol.6, No.5, pp.637-648
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TI: The ab initio neon-water potential-energy surface and its
relationship with the hydrophobic hydration shell
AU: Bagno_A
JN: JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS, 1998,
Vol.94, No.17, pp.2501-2504
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TI: Darwin and Mendel versus Watson and Crick
AU: Pollack_R
JN: FASEB JOURNAL, 1998, Vol.12, No.2, pp.149-150
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TI: Peptide bonds revisited
AU: Weiss_MS, Jabs_A, Hilgenfeld_R
JN: NATURE STRUCTURAL BIOLOGY, 1998, Vol.5, No.8, p.676
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TI: The energy landscape in non-biological and biological
molecules
AU: Frauenfelder_H, Leeson_DT
JN: NATURE STRUCTURAL BIOLOGY, 1998, Vol.5, No.9, pp.757-759
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TI: New techniques in structural NMR - anisotropic interactions
AU: Prestegard_JH
JN: NATURE STRUCTURAL BIOLOGY, 1998, Vol.5, No.SS, pp.517-522
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TI: The instability of authorship: credit and responsibility
in comtemporary biomedicine
AU: Biagioli_M
JN: FASEB JOURNAL, 1998, Vol.12, No.1, pp.3-16
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TI: The conscious mind: in search of a fundamental theory -
Chalmers,DJ
AU: Gregory_F
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.66, No.1,
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TI: A fair method for resetting the target in interrupted one-day
cricket matches
AU: Duckworth_FC, Lewis_AJ
JN: JOURNAL OF THE OPERATIONAL RESEARCH SOCIETY, 1998, Vol.49,
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TI: NMR methods blossom
AU: Wilson_EK
JN: CHEMICAL AND ENGINEERING NEWS, SEPT 28, 1998
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TI: Protein structure prediction by threading. Why it works and
why it does not.
AU: Mirny_LA, Shakhnovich_EI
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.283, No.2, pp.507-526
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TI: Electrostatic steering and ionic tethering in enzyme-ligand
binding: Insights from simulations
AU: Wade_RC, Gabdoulline_RR, Ludemann_SK, Lounnas_V
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
STATES OF AMERICA, 1998, Vol.95, No.11, pp.5942-5949
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TI: Computational biomolecular science
AU: Wolynes_PG
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
STATES OF AMERICA, 1998, Vol.95, No.11, p.5848
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TI: The age of the universe, dark matter, and structure formation
AU: Schramm_DN
JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED
STATES OF AMERICA, 1998, Vol.95, No.1, p.1
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TI: Research: Protein structure - Sieves in sequence
AU: Fersht_AR
JN: SCIENCE, 1998, Vol.280, No.5363, p.541
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TI: Influence of environment on proton-transfer mechanisms in
model triads from theoretical calculations
AU: Li_GS, Maigret_B, Rinaldi_D, Ruizlopez_MF
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.15,
pp.1675-1688
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TI: Molecular quantum similarity measures as an alternative to log
p values in QSAR studies
AU: Amat_L, CarboDorca_R, Ponec_R
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.14,
pp.1575-1583
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TI: Assessing energy functions for flexible docking
AU: Vieth_M, Hirst_JD, Kolinski_A, Brooks_CL
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.14,
pp.1612-1622
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TI: Automated docking using a Lamarckian genetic algorithm and an
empirical binding free energy function
AU: Morris_GM, Goodsell_DS, Halliday_RS, Huey_R, Hart_WE, Belew_RK,
Olson_AJ
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.14,
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TI: Pairwise calculation of protein solvent-accessible surface areas
AU: Street_AG, Mayo_SL
JN: FOLDING & DESIGN, 1998, Vol.3, No.4, pp.253-258
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TI: Structural evidence for the aromatic-(i+1) amine hydrogen bond
in peptides: L-Tyr-L-Tyr-L-Leu monohydrate
AU: Steiner_T
JN: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY,
1998, Vol.54, No.Pt4, pp.584-588
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TI: Structure of an enantiomeric protein, D-monellin at 1.8 angstrom
resolution
AU: Hung_LW, Kohmura_M, Ariyoshi_Y, Kim_SH
JN: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998,
Vol.54, No.Pt4, pp.494-500
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TI: Use of molecular overlap to predict intermolecular repulsion in
N center dot center dot center dot H-O hydrogen bonds
AU: Nobeli_I, Price_SL, Wheatley_RJ
JN: MOLECULAR PHYSICS, 1998, Vol.95, No.3, pp.525-537
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TI: Theoretical investigations of conformational aspects of polymorphism.
Part 1: O-acetamidobenzamide
AU: Buttar_D, Charlton_MH, Docherty_R, Starbuck_J
JN: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, 1998, No.4,
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TI: Generation of crystal structures of acetic acid and its halogenated
analogs
AU: Payne_RS, Roberts_RJ, Rowe_RC, Docherty_R
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1998, Vol.19, No.1, pp.1-20
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TI: Predictions of crystal packings for uracil, 6-azauracil, and
allopurinol: The interplay between hydrogen bonding and close packing
AU: Price_SL, Wibley_KS
JN: JOURNAL OF PHYSICAL CHEMISTRY A, 1997, Vol.101, No.11, pp.2198-2206
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TI: Advancing beyond the atom-centered model in additive and
nonadditive molecular mechanics
AU: Dixon_RW, Kollman_PA
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, Vol.18, No. 13,
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TI: Theoretical approaches to the study of non-bonded interactions
AU: Price_SL
JN: NATO ASI, 1998 in press
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TI: Developing methods of crystal structure and polymorph prediction
AU: Price_SL
JN: NATO ASI, 1998 in press
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TI: Intermolecular forces - from the molecular charge distribution
to the molecular packing
AU: Price_SL
JN: in Theoretical Aspects and Computer Modelling (Ed Gavezzotti_A), 1997
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TI: Towards more accurate model intermolecular potentials for
organic molecules
AU: Price_SL
JN: REVIEWS IN COMPUTATIONAL CHEMISTRY, in press
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TI: An ab initio study of the conformational preferences of Hoechst 33258
in gas-phase and aqueous solution environments
AU: Aleman_C
JN: THEORETICAL CHEMISTRY ACCOUNTS, 1998, Vol.99, No.5, pp.312-319
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TI: Archetypal energy landscapes
AU: Wales_DJ, Miller_MA, Walsh_TR
JN: NATURE, 1998, Vol.394, No.6695, pp.758-760
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TI: The measurement of molecular diversity by receptor site interaction
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AU: Parks_CA, Crippen_GM, Topliss_JG
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1998, Vol.12, No.5,
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TI: THE RELAXATION OF MOLECULAR-CRYSTAL STRUCTURES USING A DISTRIBUTED
MULTIPOLE ELECTROSTATIC MODEL
AU: WILLOCK_DJ, PRICE_SL, LESLIE_M, CATLOW_CRA
JN: JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, Vol.16, No.5, pp.628-647
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TI: Empirical scoring functions. II. The testing of an empirical
scoring function for the prediction of ligand-receptor binding
affinities and the use of Bayesian regression to improve the
quality of the model
AU: Murray_CW, Auton_TR, Eldridge_MD
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1998, Vol.12, No.5,
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TI: Feature trees: a new molecular similarity measure based on tree
matching
AU: Rarey_M, Dixon_JS
JN: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1998, Vol.12, No.5,
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TI: A soft, mean-field potential derived from crystal contacts for
predicting protein-protein interactions
AU: Robert_CH, Janin_J
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.283, No.5, pp.1037-1047
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TI: A single-crystal neutron diffraction refinement of benzamide at
15 and 123 K
AU: Gao_Q, Jeffrey_GA, Ruble_JR, McMullan_RK
JN: ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 1991,
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TI: Solid-state transformations and crystal structure analysis of
alpha- and beta-o-acetamidobenzamide
AU: Errede_LA, Etter_MC, Williams_RC, Darnauer_SM
JN: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, 1981,
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TI: Methylxanthines. I. Anhydrous theophylline
AU: Ebisuzaki_Y, Boyle_PD, Smith_JA
JN: ACTA CRYSTALLOGRAPHICA SECTION C, 1997, Vol.53, pp.777-779
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TI: Ab inition study of the structure and tautomerism of internally
hydrogen-bonded aromatic carbonyls: salicylamide, salicylic acid,
and o-hydroxybenzoyl cyanide
AU: Estevez_CM, Rios_MA, Rodriguez_J
JN: STRUCTURAL CHEMISTRY, 1992, Vol3, No.6, p.381
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TI: Molecular shape, shape of the geometrically active atomic
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AU: Komninos_Y, Nicolaides_CA
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1999, Vol.71, No.1,
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TI: AB-INITIO HARTREE-FOCK STUDY OF LITHIUM AND SODIUM SULFIDES -
ELECTRONIC AND SCATTERING PROPERTIES
AU: AZAVANT_P, LICHANOT_A, RERAT_M, PISANI_C
JN: ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 1994, Vol.50,
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TI: Ab initio quantum mechanical study of the structure and stability of
the alkaline earth metal oxides and peroxides
AU: Konigstein_M, Catlow_CRA
JN: JOURNAL OF SOLID STATE CHEMISTRY, 1998, Vol.140, No.1, pp.103-115
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TI: An Hartree-Fock study of potassium adsorption in TIO_2 surfaces
AU: Muscat_J, Harrison_NM, Thornton_G
JN: PHYS. REV. B. submitted
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TI: On the use of symmetry-adapted crystalline orbitals in SCF-LCAO
periodic calculations. I. The construction of the symmetrized
orbitals
AU: ZicovichWilson_CM, Dovesi_R
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.67, No.5,
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TI: On the use of symmetry-adapted crystalline orbitals in SCF-LCAO
periodic calculations. II. Implementation of the self-consistent-
field scheme and examples
AU: ZicovichWilson_CM, Dovesi_R
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.67, No.5,
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TI: Three-dimensional Hartree-Fock crystal-orbital calculations on
conducting polymers: trans-polyacetylene and polythiophene
AU: Starikov_EB
JN: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1998, Vol.68, No.6,
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TI: Intramolecular hydrogen bonding in 2-hydroxybenzoyl compounds:
infrared spectra and quantum chemical calculations
AU: Lampert_H, Mikenda_W, Karpfen_A
JN: JOURNAL OF PHYSICAL CHEMISTRY, 1996, Vol.100, pp.7418-7425
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TI: Internal vibrations of a molecule consisting of rigid segments.
I. Non-interacting internal vibrations
AU: He_XM, Craven_BM
JN: ACTA CRYSTALLOGRAPHICA SECTION A-FUNDAMENTALS OF CRYSTALLOGRAPHY,
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TI: Potential functions for describing intermolecular interactions in
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AU: CabaleiroLago_EM, Rios_MA
JN: JOURNAL OF CHEMICAL PHYSICS, 1998, Vol.108, No.19, pp.8398-8406
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TI: Counterpoise-corrected potential energy surfaces of simple H-
bonded systems
AU: Hobza_P, Havlas_Z
JN: THEORETICAL CHEMISTRY ACCOUNTS, 1998, Vol.99, No.5-6, pp.372-377
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TI: Complexes of ammonia with propane and cyclopropane: electrostatic
guidelines for ab initio treatment
AU: Gadre_SR, Bhadane_PK
JN: THEORETICAL CHEMISTRY ACCOUNTS, 1998, Vol.100, No.5-6, pp.300-306
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TI: C-H center dot center dot center dot O hydrogen bond involving
proline residues in alpha-helices
AU: Chakrabarti_P, Chakrabarti_S
JN: JOURNAL OF MOLECULAR BIOLOGY, 1998, Vol.284, No.4, pp.867-873
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TI: The catalytic activity of xanthine oxidase: Mechanistic insights
through computer modelling
AU: Bray_MR, Deeth_RJ
JN: JOURNAL OF THE CHEMICAL SOCIETY-DALTON TRANSACTIONS, 1997, No.8,
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TI: Determinants of strand register in antiparallel beta-sheets of
proteins
AU: Hutchinson_EG, Sessions_RB, Thornton_JM, Woolfson_DN
JN: PROTEIN SCIENCE, 1998, Vol.7, No.11, pp.2287-2300
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TI: Hydrophobicity regained
AU: Karplus_PA
JN: PROTEIN SCIENCE, 1997, Vol.6, No.6, pp.1302-1307
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TI: Protein-protein recognition: Exploring the energy funnels near
the binding sites
AU: Zhang_C, Chen_J, DeLisi_C
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1999, Vol.34, No.2,
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TI: Discovery of local packing motifs in protein structures
AU: Jonassen_I, Eidhammer_I, Taylor_WR
JN: PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1999, Vol.34, No.2,
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TI: Prediction and classification of alpha-turn types
AU: Chou_KC
JN: BIOPOLYMERS, 1997, Vol.42, No.7, pp.837-853
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TI: Free energy of amide hydrogen bond formation in vacuum, in water, and
in liquid alkane solution
AU: BenTal_N, Sitkoff_D, Topol_IA, Yang_AS, Burt_SK, Honig_B
JN: JOURNAL OF PHYSICAL CHEMISTRY B, 1997, Vol.101, No.3, pp.450-457
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TI: On quantum molecular similarity measures (QMSM) and indicies (QMSI)
AU: Carbo_R, Besalu_E, Amat_L, Fradera_X
JN: JOURNAL OF MATHEMATICAL CHEMISTRY, 1996, Vol.19, pp.47-56
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Energy Ranking of Molecular Crystals Using Density Functional Theory Calculations and an Empirical van der Waals Correction
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H. Li, C.Y. Ung, C.W. Yap, Y. Xue, Z.R. Li and Y.Z. Chen
Prediction of estrogen receptor agonists and characterization of associated molecular descriptors by statistical learning methods
Journal of Molecular Graphics and Modelling 25, 313-323 (2006)
https://doi.org/10.1016/j.jmgm.2006.01.007
(06094)
Emre Karakoc, Artem Cherkasov, and S. Cenk Sahinalp
Distance based algorithms for small biomolecule classification and structural similarity search
Bioinformatics 22: e243-e251 (2006)
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(06095)
N.H. Beltran, M.A. Duarte-Mermoud, M.A. Bustos, S.A. Salah, E.A. Loyola, A.I. Pena-Neira and J.W. Jalocha
Feature extraction and classification of Chilean wines
Journal of Food Engineering 75, 1-10 (2006)
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(06096)
M Clark
Generalized Fragment-Substructure Based Property Prediction Method
J. Chem. Inf. Model., 45, 30-38 (2005)
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(06097)
L Lam & SY Suen
Application of majority voting to pattern recognition: an analysisof its behavior and performance
IEEE Transactions on, Systems, Man and Cybernetics - Part A: Systems & Humans, 27, 553-568 (1997)
(06098)
Niu Huang, Chakrapani Kalyanaraman, Katarzyna Bernacki and Matthew P. Jacobson
Molecular mechanics methods for predicting protein-ligand binding
PCCP 8, 5166-5177 (2006)
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(06099)
Bergstrom CAS, Norinder U, Luthman K, Artursson P
Molecular Descriptors Influencing Melting Point and Their Role in Classification of Solid Drugs
J. Chem. Inf. Model., 43, 1177-1185 (2003)
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(06100)
Sun H
A Universal Molecular Descriptor System for Prediction of LogP, LogS, LogBB, and Absorption
J. Chem. Inf. Model., 44, 748-757 (2004)
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(06101)
Sam P. de Visser
Can the peroxosuccinate complex in the catalytic cycle of taurine/-ketoglutarate dioxygenase (TauD) act as an alternative oxidant?
Chem Commun 171-173 (2007)
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(JBOM41)
E.O. Cannon & J.B.O. Mitchell
Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint
Lecture Notes in Bioinformatics, 4216, 173-182 (2006)
https://doi.org/10.1007/11875741
(06102)
Niclas Tue Hansen, Irene Kouskoumvekaki, Flemming Steen Jorgensen, Soren Brunak, and Svava Osk Jonsdottir
Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules
J. Chem. Inf. Model., 46, 2601-2609 (2006)
https://doi.org/10.1021/ci600292q
(06103)
Simone Sciabola, Inaki Morao, and Marcel J. de Groot
Pharmacophoric Fingerprint Method (TOPP) for 3D-QSAR Modeling: Application to CYP2D6 Metabolic Stability
J. Chem. Inf. Model., 47, 76-84 (2007)
https://doi.org/10.1021/ci060143q
(JBOM42)
Edward O. Cannon, Andreas Bender, David S. Palmer, and John B. O. Mitchell
Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport
J. Chem. Inf. Model., 46, 2369-2380 (2006)
https://doi.org/10.1021/ci0601160
(JBOM43)
Florian Nigsch, Andreas Bender, Bernd van Buuren, Jos Tissen, Eduard Nigsch, and John B. O. Mitchell
Melting Point Prediction Employing k-Nearest Neighbor Algorithms and Genetic Parameter Optimization
J. Chem. Inf. Model., 46, 2412-2422 (2006)
https://doi.org/10.1021/ci060149f
(06104)
Jose Batista and Jurgen Bajorath
Chemical Database Mining through Entropy-Based Molecular Similarity Assessment of Randomly Generated Structural Fragment Populations
J. Chem. Inf. Model., 47, 59-68 (2007)
https://doi.org/10.1021/ci600377m
(06105)
Megan S C Lim, Margaret E Hellard, Campbell K Aitken
The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute
BMJ 331:1498-1500 (2005)
(06106)
Rodolfo Pinal
Effect of molecular symmetry on melting temperature and solubility
Org. Biomol. Chem., 2, 2692-2699 (2004)
https://doi.org/10.1039/B407105K
(07001)
Helene Brion and Carl Moser
Electronic Structure of Carbon Monoxide
J Chem Phys 32, 1194-1199 (1960)
(JBOM44)
GL Holliday, DE Almonacid, GJ Bartlett, NM O'Boyle, JW Torrance, P Murray-Rust, JBO Mitchell & JM Thornton,
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms,
Nucleic Acids Research, 35, D515-D520 (2007)
https://doi.org/10.1093/nar/gkl774
(JBOM45)
DS Palmer, NM O'Boyle, RC Glen & JBO Mitchell,
Random Forest Models to Predict Aqueous Solubility,
Journal of Chemical Information and Modeling, 47, 150-158 (2007)
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(07002)
Arakaki A.K., Tian W. and Skolnick J.
High precision multi-genome scale reannotation of enzyme function by EFICAz
BMC Genomics 7:315 (2006)
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(07003)
Anton Schwaighofer, Timon Schroeter, Sebastian Mika, Julian Laub, Antonius ter Laak, Detlev Sulzle, Ursula Ganzer, Nikolaus Heinrich, and Klaus-Robert Muller
Accurate Solubility Prediction with Error Bars for Electrolytes: A Machine Learning Approach
Journal of Chemical Information and Modeling, 47, 407-424 (2007)
https://doi.org/10.1021/ci600205g
(07004)
Stephen Jelfs, Peter Ertl, and Paul Selzer
Estimation of pKa for Druglike Compounds Using Semiempirical and Information-Based Descriptors
Journal of Chemical Information and Modeling, 47, 450-459 (2007)
https://doi.org/10.1021/ci600285n
(07005)
Qing-You Zhang and Joao Aires-de-Sousa
Random Forest Prediction of Mutagenicity from Empirical Physicochemical Descriptors
Journal of Chemical Information and Modeling, 47, 1-8 (2007)
https://doi.org/10.1021/ci050520j
(07006)
Marwen Naim, Sathesh Bhat, Kathryn N. Rankin, Sheldon Dennis, Shafinaz F. Chowdhury, Imran Siddiqi, Piotr Drabik, Traian Sulea, Christopher I. Bayly, Araz Jakalian, and Enrico O. Purisima
Solvated Interaction Energy (SIE) for Scoring Protein-Ligand Binding Affinities. 1. Exploring the Parameter Space
Journal of Chemical Information and Modeling, 47, 122-133 (2007)
https://doi.org/10.1021/ci600406v
(07007)
Carolin Strobl, Anne-Laure Boulesteix, Achim Zeileis, Torsten Hothorn
Bias in random forest variable importance measures: Illustrations, sources and a solution
BMC Bioinformatics, 8, 25 (2007)
https://doi.org/10.1186/1471-2105-8-25
(JBOM46)
Chrysi Konstantinou-Kirtay, John BO Mitchell, James A Lumley
Scoring functions and enrichment: a case study on Hsp90
BMC Bioinformatics, 8, 27 (2007)
https://doi.org/10.1186/1471-2105-8-27
(07008)
John A Swets
Measuring the Accuracy of Diagnostic Systems
Science 240, 1285-1293 (1988)
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JC McLennan, AB McLay, H Grayson Smith
Atomic States and Spectral Terms
Proc Roy Soc Lond A, 112, 76-94 (1926)
(07010)
Ralph G Pearson
Concerning Jahn-Teller Effects
PNAS 72, 2104-2106 (1975)
(07011)
Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK.
Relating protein pharmacology by ligand chemistry.
Nature Biotech 25 (2), 197-206 (2007)
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(07012)
A Dokoumetzidis, P Macheras
A century of dissolution research: From Noyes and Whitney to the Biopharmaceutics Classification System
Int J Pharmaceutics 321, 1-11 (2006)
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(07013)
H Agren, J Nordgren, L Selander, C Nordling & K Siegbahn
Valence electron structure of the SF6 and CS2 molecules, studied in high resolution X-ray emission
Physica Scripta 18, 499-505 (1978)
(07014)
RA Dickson, PJ Houghton, PJ Hylands & S Gibbons
Antimicrobial, resistance-modifying effects, antioxidant and free radical scavenging activities of Mezoneuron benthamianum Baill., Securinega virosa Roxb. & Wlld. and Microglossa pyrifolia Lam.
Phytotherapy Research 20, 41-45 (2006)
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(07015)
MJ Sutcliffe & NS Scrutton
A new conceptual framework for enzyme catalysis
Hydrogen tunneling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes
Eur. J. Biochem. 269, 3096-3102 (2002)
https://doi.org/10.1046/j.1432-1033.2002.03020.x
(07016)
Laura Masgrau, Jaswir Basran, Parvinder Hothi, Michael J. Sutcliffe, and Nigel S. Scrutton
Hydrogen tunneling in quinoproteins
Archives of Biochemistry and Biophysics 428, 41-51 (2004)
(07017)
Scott Oloff, Ingo Muegge
kScore: a novel machine learning approach that is not dependent
on the data structure of the training set
J Comput Aided Mol Des, 21, 87-95 (2007)
https://doi.org/10.1007/s10822-007-9108-0
(07018)
MA Glasner, JA Gerlt, PC Babbitt
Evolution of enzyme superfamilies
Current Opinion in Chemical Biology, 10, 492-497 (2006)
https://doi.org/10.1016/j.cbpa.2006.08.012
(07019)
Olga Khersonsky, Cintia Roodveldt and Dan S Tawfik
Enzyme promiscuity: evolutionary and mechanistic aspects
Current Opinion in Chemical Biology, 10, 498-508 (2006)
https://doi.org/10.1016/j.cbpa.2006.08.011
(07020)
Copley SD
Enzymes with extra talents: moonlighting functions and catalytic promiscuity
Current Opinion in Chemical Biology, 7, 265-272 (2003)
https://doi.org/10.1016/S1367-5931(03)00032-2
(JBOM47)
E.O. Cannon, A. Amini, A. Bender, M.J.E. Sternberg, S.H. Muggleton, R.C. Glen & J.B.O. Mitchell
Support Vector Inductive Logic Programming Outperforms the Naive Bayes Classifier and Inductive Logic Programming for the Classification of Bioactive Chemical Compounds
Journal of Computer-Aided Molecular Design, 21, 269-280 (2007)
https://doi.org/10.1007/s10822-007-9113-3
(JBOM48)
N.M. O'Boyle, G.L. Holliday, D.E. Almonacid & J.B.O. Mitchell
Using Reaction Mechanism to Measure Enzyme Similarity
Journal of Molecular Biology, 368, 1484-1499 (2007)
https://doi.org/10.1016/j.jmb.2007.02.065
(07021)
Bemis G W, Murcko M A
The properties of known drugs. 1. Molecular frameworks.
J Med Chem, 39, 2887-2893 (1996)
(07022)
Jeremy L. Jenkins, Meir Glick, and John W. Davies
A 3D Similarity Method for Scaffold Hopping from Known Drugs or Natural Ligands to New Chemotypes
J. Med. Chem., 47, 6144-6159 (2004)
https://doi.org/10.1021/jm049654z
(07023)
Glenn A. Burley
Trannulenes with "In-Plane" Aromaticity: Candidates for Harvesting Light Energy
Angew. Chem. Int. Ed. 44, 3176-3178 (2005)
https://doi.org/10.1002/anie.200500362
(07024)
F R Manby, H-J Werner, T B Adler and A J May
Explicitly correlated local second-order perturbation theory with a frozen geminal correlation factor
J. Chem. Phys. 124 094103 (2006)
https://doi.org/10.1063/1.2173247
(07025)
Jennifer C. Brookes, Filio Hartoutsiou, A. P. Horsfield, and A. M. Stoneham
Could Humans Recognize Odor by Phonon Assisted Tunneling?
Phys Rev Lett 98, 038101 (2007)
https://doi.org/10.1103/PhysRevLett.98.038101
(07026)
C. S. Sell
On the Unpredictability of Odor
Angew. Chem. Int. Ed., 45, 6254-6261 (2006)
https://doi.org/10.1002/anie.200600782
(07027)
Scott C.-H. Pegg, Shoshana D. Brown, Sunil Ojha, Jennifer Seffernick, Elaine C. Meng, John H. Morris, Patricia J. Chang, Conrad C. Huang, Thomas E. Ferrin, and Patricia C. Babbitt
Leveraging Enzyme Structure-Function Relationships for Functional Inference and
Experimental Design: The Structure-Function Linkage Database
Biochemistry, 45, 2545-2555 (2006)
https://doi.org/10.1021/bi052101l
(07028)
AJ Stone
Distributed Multipole Analysis: Stability for Large Basis Sets
J. Chem. Theory Comput. 1, 1128-1132 (2005)
https://doi.org/10.1021/ct050190+
(07029)
Alston J. Misquitta and Anthony J. Stone
Distributed polarizabilities obtained using a constrained density-fitting algorithm
J. Chem. Phys. 124, 024111 (2006)
https://doi.org/10.1063/1.2150828
(07030)
Matthew Bashton & Cyrus Chothia
The Generation of New Protein Functions by the Combination of Domains
Structure, 15, 85-99 (2007)
https://doi.org/10.1016/j.str.2006.11.009
(JBOM49)
J.W. Torrance, G.L. Holliday, J.B.O. Mitchell & J.M. Thornton
The Geometry of Interactions Between Catalytic Residues and their Substrates
Journal of Molecular Biology, 369, 1140-1152 (2007)
https://doi.org/10.1016/j.jmb.2007.03.055
(07031)
Hiroshi Sawada, Kenji Takami, and Satoru Asahi
A Toxicogenomic Approach to Drug-Induced Phospholipidosis: Analysis of Its Induction Mechanism and Establishment of a Novel in Vitro Screening System
Toxicological Sciences, 83, 282-292 (2005)
https://doi.org/10.1093/toxsci/kfh264
(07032)
Han van de Waterbeemd and Eric Gifford
ADMET in silico modelling: towards prediction paradise?
Nat Rev Drug Discov. 2, 192-204 (2003)
https://doi.org/10.1038/nrd1032
(07033)
Ploemen JP, Kelder J, Hafmans T, van de Sandt H, van Burgsteden JA, Saleminki PJ, van Esch E
Use of physicochemical calculation of pKa and CLogP to predict phospholipidosis-inducing potential: a case study with structurally related piperazines
Exp Toxic Pathol 55, 347-355 (2004)
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(07034)
Smith DA
Hello Drug Discovery, I am from Insilico, take me to your President
Drug Discovery Today, 7, 1080-1081 (2002)
(07035)
Stephen R. Johnson, Xue-Qing Chen, Denette Murphy, and Olafur Gudmundsson
A Computational Model for the Prediction of Aqueous Solubility That Includes Crystal Packing, Intrinsic Solubility, and Ionization Effects
Molecular Pharmaceutics, 4, 513-523 (2007)
https://doi.org/10.1021/mp070030+
(07036)
Kai Luder, Lennart Lindfors, Jan Westergren, Sture Nordholm, and Roland Kjellander
In Silico Prediction of Drug Solubility. 3. Free Energy of Solvation in Pure Amorphous Matter
J. Phys. Chem. B, 111, 7303-7311 (2007)
https://doi.org/10.1021/jp071687d
(07037)
Jan Westergren, Lennart Lindfors, Tobias Hoglund, Kai Luder, Sture Nordholm, and Roland Kjellander
In Silico Prediction of Drug Solubility: 1. Free Energy of Hydration
J. Phys. Chem. B, 111, 1872-1882 (2007)
https://doi.org/10.1021/jp064220w
(07038)
Kai Luder, Lennart Lindfors, Jan Westergren, Sture Nordholm, and Roland Kjellander
In Silico Prediction of Drug Solubility: 2. Free Energy of Solvation in Pure Melts
J. Phys. Chem. B, 111, 1883-1892 (2007)
https://doi.org/10.1021/jp0642239
(07039)
Stefano Pieraccini; Luigi Burgi; Alessandro Genoni; Anna Benedusi; Maurizio Sironi
Atomic level description of the protecting effect of osmolytes against thermal denaturation of proteins
Chemical Physics Letters, 438, 298-303 (2007)
https://doi.org/10.1016/j.cplett.2007.03.007
(07040)
Jordi Ribas-Arino & Juan J. Novoa
The mechanism for the reversible oxygen addition to heme. A theoretical CASPT2 study
Chemical Communications 3160-3162 (2007)
https://doi.org/10.1039/b704871h
(07041)
Mark J. Reasor & Sam Kacew
Drug-Induced Phospholipidosis: Are There Functional Consequences?
Experimental Biology and Medicine 226:825-830 (2001)
(07042)
PJ Ballester & WG Richards
Ultrafast shape recognition for similarity search in molecular databases
Proc. R. Soc. A, 463, 1307-1321 (2007)
https://doi.org/10.1098/rspa.2007.1823
(07043)
Hongzhou Zhang, Howard Y. Ando, Linna Chen, and Pil H. Lee
On-the-Fly Selection of a Training Set for Aqueous Solubility Prediction
Molecular Pharmaceutics 4, 489-497 (2007)
https://doi.org/10.1021/mp0700155
(07044)
Kaori Tomizawa, Kiyohiko Sugano, Hiroshi Yamada & Ikuo Horii
Physicochemical and cell-based approach for early screening of phospholipidosis-inducing potential
The Journal of Toxicological Sciences, 31, 315-324 (2006)
https://doi.org/10.2131/jts.31.315
(07045)
Patricia C. Babbitt and John A. Gerlt
Understanding Enzyme Superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities.
J. Biol. Chem., 272, 30591-30594 (1997)
(07046)
Jason D. Thompson, Christopher J. Cramer, and Donald G. Truhlar
Predicting aqueous solubilities from aqueous free energies of solvation
and experimental or calculated vapor pressures of pure substances
J Chem Phys, 119, 1661-1670 (2003)
https://doi.org/10.1063/1.1579474
(07047)
D. Zakarya, M. Chastrette, M. Tollabi & S. Fkih-Tetouani
Structure.camphor odour relationships using the Generation and
Selection of Pertinent Descriptors approach
Chemometrics and Intelligent Laboratory Systems 48, 35-46 (1999)
(07048)
Johannes C. Hermann, Ricardo Marti-Arbona, Alexander A. Fedorov, Elena Fedorov, Steven C. Almo, Brian K. Shoichet & Frank M. Raushel
Structure-based activity prediction for an enzyme of unknown function
Nature, 448, 775-779 (2007)
https://doi.org/10.1038/nature05981
(07049)
JoAnne Stubbe
Computational biochemistry: Models of transition
Nature, 448, 762 (2007)
https://doi.org/10.1038/448762a
(07050)
Pedro Cintas
Chemical reaction to the many-worlds hypothesis
Nature, 448, 749 (2007)
https://doi.org/10.1038/448749c
(07051)
Mark Buchanan
See me here, see me there
Nature, 448, 15 (2007)
https://doi.org/10.1038/448015a
(07052)
Junmei Wang, George Krudy, Tingjun Hou, Wei Zhang, George Holland, and Xiaojie Xu
Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis
Journal of Chemical Information and Modeling, 47, 1395-1404 (2007)
https://doi.org/10.1021/ci700096r
(07053)
Dennis J Pelletier, Daniel Gehlhaar, Anne Tilloy-Ellul, Theodore O. Johnson, and Nigel Greene
Evaluation of a Published in Silico Model and Construction of a Novel Bayesian Model for Predicting Phospholipidosis Inducing Potential
Journal of Chemical Information and Modeling, 47, 1196-1205 (2007)
https://doi.org/10.1021/ci6004542
(07054)
Carl R. Woese
On the evolution of cells
Proc. Natl. Acad. Sci. USA, 99, 8742-8747 (2002)
https://doi.org/10.1073/pnas.132266999
(07055)
Lian Yu
Survival of the fittest polymorph: how fast nucleater can lose to fast grower
CrystEngComm, 9, 847-851 (2007)
https://doi.org/10.1039/b709260c
(07056)
Florian Nigsch, Werner Klaffke & Silvia Miret
In vitro models for processes involved in intestinal absorption
Expert Opin. Drug Metab. Toxicol. 3, 545-556 (2007)
https://doi.org/10.1517/17425225.3.4.545
(07057)
W. D. Samuel Motherwell, Gregory P. Shields and Frank H. Allen
Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural Database
Acta Crystallographa B56, 856-871 (2000)
https://doi.org/10.1107/S0108768100007230
(07058)
Juan A. G. Ranea, Antonio Sillero, Janet M. Thornton, Christine A. Orengo
Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)
J Mol Evol, 63, 513-525 (2006)
https://doi.org/10.1007/s00239-005-0289-7
(07059)
Coombes DS, Catlow CRA, Gale JD, Rohl AL, Price SL
Calculation of Attachment Energies and Relative Volume Growth Rates As an Aid to Polymorph Prediction
Cryst. Growth Des., 5, 879-885 (2005)
https://doi.org/10.1021/cg049707d
(07060)
JAG Ranea
Micro(be)-economics
Heredity 96, 337-338 (2006)
https://doi.org/10.1038/sj.hdy.6800766
(JBOM50)
G.L. Holliday, D.E. Almonacid, J.B.O. Mitchell & J.M. Thornton
The Chemistry of Protein Catalysis
Journal of Molecular Biology, 372, 1261-1277 (2007)
https://doi.org/10.1016/j.jmb.2007.07.034
(07061)
Andrew R. Leach, Brian K. Shoichet, and Catherine E. Peishoff
Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps
Journal of Medicinal Chemistry, 49, 5851-5855 (2006)
https://doi.org/10.1021/jm060999m
(07062)
Ingo Muegge
PMF Scoring Revisited
Journal of Medicinal Chemistry, 49, 5895-5902 (2006)
https://doi.org/10.1021/jm050038s
(07063)
Gregory L. Warren, C. Webster Andrews, Anna-Maria Capelli, Brian Clarke, Judith LaLonde, Millard H. Lambert, Mika Lindvall, Neysa Nevins, Simon F. Semus, Stefan Senger, Giovanna Tedesco, Ian D. Wall, James M. Woolven, Catherine E. Peishoff, and Martha S. Head
A Critical Assessment of Docking Programs and Scoring Functions
Journal of Medicinal Chemistry, 49, 5912-5931 (2006)
https://doi.org/10.1021/jm050362n
(07064)
Jahanbakhsh Ghasemi and Saadi Saaidpour
QSPR Prediction of Aqueous Solubility of Drug-Like Organic Compounds
Chem. Pharm. Bull. 55, 669-674 (2007)
https://doi.org/10.1248/cpb.55.669
(07065)
Alexander Tropsha, Paola Gramatica & Vijay K. Gombar
The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models
QSAR & Combinatorial Science, 22, 69-77 (2003)
https://doi.org/10.1002/qsar.200390007
(07066)
Eros, D.; Kovesdi, I.; Orfi, L.; Takacs-Novak, K.; Acsady, G.; Keri, G.
Reliability of logP predictions based on calculated molecular descriptors: a critical review
Curr. Med. Chem., 9, 1819-1829 (2002)
(07067)
Tetko, I. V.; Bruneau, P.
Application of ALOGPS to predict 1-octanol/water distribution coefficients, logP, and logD, of AstraZeneca in-house database,
J. Pharm. Sci., 93, 3103-3110 (2004)
https://doi.org/10.1002/jps.20217
(07068)
Andrew G McDonald, Sinead Boyce, Gerard P Moss, Henry BF Dixon & Keith F Tipton
ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature
BMC Biochemistry 8:14 (2007)
https://doi.org/10.1186/1471-2091-8-14
(07069)
Srinivasa S. Godavarthy, Robert L. Robinson, Jr., and Khaled A. M. Gasem
An Improved Structure-Property Model for Predicting Melting-Point Temperatures
Ind. Eng. Chem. Res., 45, 5117-5126 (2006)
https://doi.org/10.1021/ie051130p
(07070)
Pier Federico Gherardini, Mark N. Wass, Manuela Helmer-Citterich and Michael J.E. Sternberg
Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
Journal of Molecular Biology, 372, 817-845 (2007)
https://doi.org/10.1016/j.jmb.2007.06.017
(07071)
Charlie Everitt
Database rights: The Advocate General issues her opinion in British Horseracing Board v. William Hill
Computer Law & Security Report 20, 405-407 (2004)
https://doi.org/10.1016/S0267-3649(04)00074-3
(07072)
Nozomi Nagano, Tamotsu Noguchi and Yutaka Akiyama
Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database
PROTEINS: Structure, Function, and Bioinformatics, 66, 147-159 (2007)
https://doi.org/10.1002/prot.21193
(07073)
Gail J. Bartlett, Neera Borkakoti and Janet M. Thornton
Catalysing New Reactions during Evolution: Economy of Residues and Mechanism
Journal of Molecular Biology, 331, 829-860 (2003)
https://doi.org/10.1016/S0022-2836(03)00734-4
(07074)
Christoph Rucker, Gerta Rucker, and Markus Meringer
y-Randomization and Its Variants in QSPR/QSAR
J. Chem. Inf. Model., 47, 2345-2357 (2007)
https://doi.org/10.1021/ci700157b
(07075)
Wei Deng, Curt Breneman & Mark J. Embrechts
Predicting Protein-Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine-Learning Methods
Journal of Chemical Information and Modeling, 44, 699-703 (2004)
https://doi.org/10.1021/ci034246+
(07076)
James R. Arnold, Keith W. Burdick, Scott C.-H. Pegg, Samuel Toba, Michelle L. Lamb & Irwin D. Kuntz
SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design
Journal of Chemical Information and Modeling, 44, 2190-2198 (2004)
https://doi.org/10.1021/ci049814f
(07077)
HL Woodcock, M Hodoscek & BR Brooks,
Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms
J. Phys. Chem. A, 111, 5720-5728 (2007)
https://doi.org/10.1021/jp0714217
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AD Favia, I Nobeli, F Glaser & JM Thornton,
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Breeding racehorses: what price good genes?
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Prediction of Melting Points of Organic Compounds Using Extreme Learning Machines
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Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions
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Rate-Limited Steps of Human Oral Absorption and QSAR Studies
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Evaluation of Human Intestinal Absorption Data and Subsequent Derivation of a Quantitative Structure-Activity Relationship (QSAR) with the Abraham Descriptors
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Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
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Quantum Mechanical Continuum Solvation Models
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Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations
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A QSAR study on relationship between structure of sulfonamides and their carbonic anhydrase inhibitory activity using the eigenvalue (EVA) method
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Computational analysis of membrane proteins: the largest class of drug targets
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Case Studies in the use of ROC Curve Analysis for Sensor-Based Estimates in Human Computer Interaction
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A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
Bioinformatics, 26, 1169-1175 (2010)
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Karel Berka, Roman Laskowski, Kevin E. Riley, Pavel Hobza, Jiri Vondrasek
Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures
J. Chem. Theory Comput., 5, 982-992 (2009)
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Ralph Kuhne, Ralf-Uwe Ebert, and Gerrit Schuurmann
Chemical Domain of QSAR Models from Atom-Centered Fragments
J. Chem. Inf. Model., 49, 2660-2669 (2009)
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Natasja Brooijmans, Dominick Mobilio, Gary Walker, Ramaswamy Nilakantan, Rajiah A. Denny, Eric Feyfant, David Diller, Jack Bikker and Christine Humblet
A structural informatics approach to mine kinase knowledge bases
Drug Discovery Today, 15, 203-209 (2010)
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Luis Simon and Jonathan M. Goodman
Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes
J. Org. Chem., 75, 1831-1840 (2010)
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Burkhard Rost
Enzyme Function Less Conserved than Anticipated
Journal of Molecular Biology, 318, 595-608 (2002)
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Arie Ben-David
Comparison of classification accuracy using Cohen's Weighted Kappa
Expert Systems with Applications, 34, 825-832 (2008)
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Stephen Winters-Hilt, Anil Yelundur, Charlie McChesney and Matthew Landry
Support Vector Machine Implementations for Classification & Clustering
BMC Bioinformatics, 7 (Suppl 2):S4 (2006)
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Emanuele Perola
An Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs
J. Med. Chem., 53, 2986-2997 (2010)
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Richard Lonsdale, Kara E. Ranaghan and Adrian J. Mulholland
Computational enzymology
Chem. Commun., 46, 2354-2372 (2010)
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Benson M Spowage, Craig L Bruce and Jonathan D Hirst
Interpretable correlation descriptors for quantitative structure-activity relationships
Journal of Cheminformatics 1:22 (2009)
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Bruce, C. L.; Melville, J. L.; Pickett, S. D.; Hirst, J. D.
Contemporary QSAR Classifiers Compared
Journal of Chemical Information and Modeling, 47, 219-227 (2007)
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Sylvia E. McLain, Alan K. Soper, Isabella Daidone, Jeremy C. Smith, Anthony Watts
Charge-Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution
Angewandte Chemie International Edition, 47, 9059-9062 (2008)
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Andreas Jansson and Mats Jirstrand
Biochemical modeling with Systems Biology Graphical Notation
Drug Discovery Today, 15, 365-370 (2010)
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Barry G. Hall, Miriam Barlow
Evolution of the serine beta-lactamases: past, present and future
Drug Resistance Updates, 7, 111-123 (2004)
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Nuno M. Garrido, Miguel Jorge, Antonio J. Queimada, Ioannis G. Economou and Eugenia A. Macedo
Molecular simulation of the hydration Gibbs energy of barbiturates
Fluid Phase Equilibria, 289, 148-155 (2010)
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Concu, R.; Dea-Ayuela, M. A.; Perez-Montoto, L. G.; Prado-Prado, F. J.; Uriarte, E.; Bolas-Fernandez, F.; Podda, G.; Pazos, A.; Munteanu, C. R.; Ubeira, F. M.
3D entropy and moments prediction of enzyme classes and experimental-theoretic study of peptide fingerprints in Leishmania parasites
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, 1794, 1784-1794 (2009)
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Umesh M. Hanumegowda, Gottfried Wenke, Alicia Regueiro-Ren, Roumyana Yordanova, John P. Corradi, Stephen P. Adams
Phospholipidosis as a Function of Basicity, Lipophilicity, and Volume of Distribution of Compounds
Chemical Research in Toxicology, 23, 749-755 (2010)
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Panagiotis G. Karamertzanis,.Paolo Raiteri, and Amparo Galindo
The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration
J. Chem. Theory Comput., 6, 1590-1607 (2010)
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Maja Divkovic, Camilla K. Pease, G. Frank Gerberick and David A. Basketter
Hapten-protein binding: from theory to practical application in the in vitro prediction of skin sensitization
Contact Dermatitis, 53, 189-200 (2005)
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David W. Roberts and Aynur O. Aptula
Determinants of skin sensitisation potential
J. Appl. Toxicol., 28, 377-387 (2008)
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Volker Egelhofer, Ida Schomburg, Dietmar Schomburg
Automatic Assignment of EC Numbers
PLoS Computational Biology, 6, e1000661 (2010)
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Munikumar R. Doddareddy, Elisabeth C. Klaasse, Shagufta, Adriaan P. Ijzerman, and Andreas Bender
Prospective Validation of a Comprehensive In silico hERG Model and its Applications to Commercial Compound and Drug Databases
ChemMedChem, 5, 716-729 (2010)
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Gavin Maxwell, Maja Aleksic, Aynur Aptula, Paul Carmichael, Julia Fentem, Nicola Gilmour, Cameron MacKay, Camilla Pease, Ruth Pendlington, Fiona Reynolds, Daniel Scott, Guy Warner and Carl Westmoreland
Assuring Consumer Safety Without Animal Testing: A Feasibility Case Study for Skin Sensitisation
Altern Lab Anim., 36, 557-568 (2008)
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Pierre Aeby, Takao Ashikaga, Walter Diembeck, Dietmar Eschrich, Frank Gerberick, Ian Kimber, Monique Marrec-Fairley, Gavin Maxwell, Jean-Marc Ovigne, Hitoshi Sakaguchi, Magalie Tailhardat and Silvia Teissier
The COLIPA strategy for the development of in vitro alternatives: Skin sensitisation
Proc. 6th World Congress on Alternatives & Animal Use in the Life Sciences, Tokyo, Japan, 2007
AATEX 14, Special Issue, 375-379 (2008)
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Weidong Tian and Jeffrey Skolnick
How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?
Journal of Molecular Biology, 333, 863-882 (2003)
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R. F. Freitas, R. L. Bauab, and C. A. Montanari
Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4
J. Chem. Inf. Model., 50, 97-109 (2010)
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S. E. Saravanan, R. Karthi, K. Sathish, K. Kokila, R. Sabarinathan and K. Sekar
MLDB: macromolecule ligand database
J. Appl. Cryst., 43, 200-202 (2010)
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Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang, Xian Chen, Hong-Dong Li
Prediction of aqueous solubility of druglike organic compounds using partial least squares, back-propagation network and support vector machine
Journal of Chemometrics, 24, 584-595 (2010)
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Salvatore Millefiori, Andrea Alparone
Electronic properties of neuroleptics: ionization energies of benzodiazepines
Journal of Molecular Modeling 17, 281-287 (2011)
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Xiaoying Hu, Aixia Yan, Tianwei Tan, Oliver Sacher, Johann Gasteiger
Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods
Journal of Chemical Information and Modeling, 50, 1089-1100 (2010)
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Sean Ekins, J. Dana Honeycutt, James T. Metz
Evolving molecules using multi-objective optimization: applying to ADME/Tox
Drug Discovery Today, 15, 451-460 (2010)
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Yang, S.-Y.
Pharmacophore modeling and applications in drug discovery: challenges and recent advances
Drug Discovery Today, 15, 444-450 (2010)
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Nasrin Jahan, Jane A. Potter, Md. Arif Sheikh, Catherine H. Botting, Sally L. Shirran, Nicholas J. Westwood and Garry L. Taylor
Insights into the Biosynthesis of the Vibrio cholerae Major Autoinducer CAI-1 from the Crystal Structure of the PLP-Dependent Enzyme CqsA
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Riadh Hammami and Ismail Fliss
Current trends in antimicrobial agent research: chemo- and bioinformatics approaches
Drug Discovery Today, 15, 540-546 (2010)
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Andreas Bender, Josef Scheiber, Meir Glick, John W. Davies, Kamal Azzaoui, Jacques Hamon, Laszlo Urban, Steven Whitebread, Jeremy L. Jenkins
Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure
ChemMedChem, 2, 861-873 (2007)
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Fischer, J. D.; Holliday, G. L.; Thornton, J. M.
The CoFactor database: Organic cofactors in enzyme catalysis
Bioinformatics, 26, 2496-2497 (2010)
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Alakoskela, J. M.; Vitovic, P.; Kinnunen, P. K. J.
Screening for the Drug-Phospholipid Interaction: Correlation to Phospholipidosis
ChemMedChem, 4, 1224-1251 (2009)
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Andreas Klamt, Uwe Huniar, Simon Spycher, and Jorg Keldenich
COSMOmic: A Mechanistic Approach to the Calculation of Membrane-Water Partition Coefficients and Internal Distributions within Membranes and Micelles
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Predicting Phospholipidosis using Machine Learning
Molecular Pharmaceutics, 7, 1708-1714 (2010)
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Sarah L. Price, Maurice Leslie, Gareth W. A. Welch, Matthew Habgood, Louise S. Price, Panagiotis G. Karamertzanis and Graeme M. Day
Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials
Phys. Chem. Chem. Phys., 12, 8478-8490 (2010)
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Redfern WS, Carlsson L, Davis AS, Lynch WG, MacKenzie I, Palethorpe S, Siegl PK, Strang I, Sullivan AT, Wallis R, Camm AJ, Hammond TG
Relationships between preclinical cardiac electrophysiology, clinical QT interval prolongation and torsade de pointes for a broad range of drugs: evidence for a provisional safety margin in drug development
Cardiovasc Res., 58, 32-45 (2003)
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Dariusz Plewczynski, Michal Lazniewski, Marcin Von V. Grotthuss, Leszek Rychlewski, Krzysztof Ginalski
VoteDock: Consensus Docking Method for Prediction of Protein-Ligand Interactions
J Comput Chem 32, 568-581 (2011)
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Dariusz Plewczynski, Michal Lazniewski, Rafal Augustyniak, Krzysztof Ginalski
Can We Trust Docking Results? Evaluation of Seven Commonly Used Programs on PDBbind Database
J Comput Chem 32, 742-745 (2011)
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Andrea Johnston, Blair F. Johnston, Alan R. Kennedy and Alastair J. Florence
Targeted crystallisation of novel carbamazepine solvates based on a retrospective Random Forest classification
CrystEngComm, 10, 23-25 (2008)
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Christian Kramer and Peter Gedeck
Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets
J. Chem. Inf. Model. 50, 1961-1969 (2010)
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Latifa Chebil, Christophe Chipot, Fabien Archambault, Catherine Humeau, Jean M. Engasser, Mohamed Ghoul, Francois Dehez
Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents
Journal of Physical Chemistry B, 114, 12308-12313 (2010)
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Chih-Wei Hsu & Chih-Jen Lin
A comparison of methods for multiclass support vector machines
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John P. Overington, Bissan Al-Lazikani, Andrew L. Hopkins
How many drug targets are there?
Nature Reviews Drug Discovery, 5, 993-996 (2006)
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M. Mori, N. Ogawa, K. Tanikawa, S. Dodo, S. Shibayama, S. Yokoyama, A. Tanaka
Contribution of structural biology to clinically validated target proteins
Drug Discovery Today, 13, 469-472 (2008)
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Sheng-You Huang, Sam Z. Grinter, Xiaoqin Zou
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions
Phys. Chem. Chem. Phys., 12, 12899-12908 (2010)
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David T.F Dryden, Andrew R Thomson, and John H White
How much of protein sequence space has been explored by life on Earth?
J R Soc Interface, 5, 953-956 (2008)
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David S Palmer, Andrey I Frolov, Ekaterina L Ratkova and Maxim V Fedorov
Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction
J. Phys.: Condens. Matter 22, 492101 (2010)
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Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou and Hai-Peng Li
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
BMC Bioinformatics, 11:293 (2010)
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Ekaterina L. Ratkova, Gennady N. Chuev, Volodymyr P. Sergiievskyi, Maxim V. Fedorov
An Accurate Prediction of Hydration Free Energies by Combination of Molecular Integral Equations Theory with Structural Descriptors
The Journal of Physical Chemistry B, 114, 12068-12079 (2010)
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Kai Luder, Lennart Lindfors, Jan Westergren, Sture Nordholm, Rasmus Persson, Mikaela Pedersen
In silico prediction of drug solubility: 4. Will simple potentials suffice?
J. Comput. Chem., 30, 1859-1871 (2009)
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M. Stuart Armstrong, Garrett M. Morris, Paul W. Finn, Raman Sharma, Loris Moretti, Richard I. Cooper, W. Graham Richards
ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics
J Comput Aided Mol Des, 24, 789-801 (2010)
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Aaron J Ihde
The Karlsruhe Congress: A centennial retrospective
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Nick Bostrom
Are You Living In a Computer Simulation?
Philosophical Quarterly, 53, 243-255 (2003)
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Pedro J Ballester
Ultrafast shape recognition: method and applications
Future Med. Chem. 3, 65-78 (2011)
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A. P. Harding, D. C. Wedge, and P. L. A. Popelier
pKa Prediction from Quantum Chemical Topology Descriptors
J. Chem. Inf. Model., 49, 1914-1924 (2009)
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Luna De Ferrari, Stuart Aitken, Jano van Hemert, Igor Goryanin
Multi-label prediction of enzyme classes using InterPro signatures
Proceedings of the Fourth International Workshop on Machine Learning in Systems Biology, Edinburgh 2010
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Allan G Harrison
John Dalton's atomic theory: Using the history and nature of science to teach particle concepts?
Australian Association for Research in Education, Brisbane, 2-5 December, 2002.
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Seiji Tsuzuki, Hideo Orita, Kazumasa Honda, Masuhiro Mikami
First-Principles Lattice Energy Calculation of Urea and Hexamine Crystals by a Combination of Periodic DFT and MP2 Two-Body Interaction Energy Calculations
The Journal of Physical Chemistry B, 114, 6799-6805 (2010)
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Daniela Wieser, Irene Papatheodorou, Matthias Ziehm, Janet M. Thornton
Computational biology for ageing
Phil Trans R Soc B, 366, 51-63 (2011)
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Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing
Journal of Chemical Information and Modeling, 51, 408-419 (2011)
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Slavica Eric, Marko Kalinic, Aleksandar Popovic, Halid Makic, Elvisa Civic, Merja Bektasevic
The importance of the accuracy of the experimental data for the prediction of solubility
Journal of the Serbian Chemical Society, 75, 483-495 (2010)
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Weiwei Shi, Andrej Bugrim, Yuri Nikolsky, Tatiana Nikolskya, Richard J. Brennan
Characteristics of Genomic Signatures Derived Using Univariate Methods and Mechanistically Anchored Functional Descriptors for Predicting Drug- and Xenobiotic-Induced Nephrotoxicity
Toxicology Mechanisms and Methods, 18, 267-276 (2008)
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J.B.O. Mitchell
Informatics, machine learning and computational medicinal chemistry
Future Medicinal Chemistry, 3, 451-467 (2011)
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Karsten M. Borgwardt, Cheng Soon Ong, Stefan Schonauer, S. V. N. Vishwanathan, Alex J. Smola and Hans-Peter Kriegel
Protein function prediction via graph kernels
Bioinformatics, 21, i47-i56 (2005)
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Alison L. Cuff, Ian Sillitoe, Tony Lewis, Andrew B. Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David Jones, Janet Thornton, Christine A. Orengo
Extending CATH: increasing coverage of the protein structure universe and linking structure with function
Nucleic Acids Research, 39, D420-D426 (2011)
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Thorsten Joachims, Thomas Finley and Chun-Nam John Yu
Cutting-plane training of structural SVMs
Mach Learn 77, 27-59 (2009)
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Peter Li, Joseph Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick Dunn, Farid Khan, Naglis Malys, Hanan Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, Jill Wishart, David Broomhead, Carole Goble, Simon Gaskell, Douglas Kell, Hans Westerhoff, Pedro Mendes, Norman Paton
Systematic integration of experimental data and models in systems biology
BMC Bioinformatics, 11, 582 (2010)
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Ruoyu Li, J. Axel Zeitler, Daniele Tomerini, Edward P. J. Parrott, Lynn F. Gladden, Graeme M. Day
A study into the effect of subtle structural details and disorder on the terahertz spectrum of crystalline benzoic acid
Phys. Chem. Chem. Phys., 12, 5329-5340 (2010)
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Karl Box, John E Comer, Tom Gravestock, Martin Stuart
New Ideas about the Solubility of Drugs
Chemistry & Biodiversity, 6, 1767-1788 (2009)
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Richard L. Marchese Robinson, Robert C. Glen, John B. O. Mitchell
Development and Comparison of hERG Blocker Classifiers: Assessment on Different Datasets Yields Markedly Different Results
Mol. Inf., 30, 443-458 (2011)
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G.L. Holliday, J.D. Fischer, J.B.O. Mitchell & J.M. Thornton
Characterising the complexity of enzymes based on their mechanisms and structures using a bio-computational analysis
FEBS Journal, 278, 3835-3845 (2011)
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Katarzyna R. Przybylak & Mark T. D. Cronin
In Silico Studies of the Relationship Between Chemical Structure and Drug Induced Phospholipidosis
Molecular Informatics, 30, 415-429 (2011)
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David S. Palmer, Volodymyr P. Sergiievskyi, Frank Jensen, and Maxim V. Fedorov
Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model
J. Chem. Phys. 133, 044104 (2010)
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Andrey I. Frolov, Ekaterina L. Ratkova, David S. Palmer, and Maxim V. Fedorov
Hydration Thermodynamics Using the Reference Interaction Site Model: Speed or Accuracy?
J. Phys. Chem. B, 115, 6011-6022 (2011)
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Shuangliang Zhao, Zhehui Jin, and Jianzhong Wu
New Theoretical Method for Rapid Prediction of Solvation Free Energy in Water
J. Phys. Chem. B, 115, 6971-6975 (2011)
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Matthew T. Geballe, A. Geoffrey Skillman, Anthony Nicholls, J. Peter Guthrie & Peter J. Taylor
The SAMPL2 blind prediction challenge: introduction and overview
J Comput Aided Mol Des, 24, 259-279 (2010)
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Daniel E Almonacid and Patricia C Babbitt
Toward mechanistic classification of enzyme functions
Current Opinion in Chemical Biology, 15, 435-442 (2011)
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Elaine C Meng and Patricia C Babbitt
Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies
Current Opinion in Structural Biology, 21, 391-397 (2011)
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David S. Palmer, Andrey I. Frolov, Ekaterina L. Ratkova, Maxim V. Fedorov
Toward a Universal Model To Calculate the Solvation Thermodynamics of Druglike Molecules: The Importance of New Experimental Databases
Molecular Pharmaceutics, 8, D776-D782 (2011)
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Andreas Klamt
The COSMO and COSMO-RS solvation models
WIREs Computational Molecular Science, 1, 699-709 (2011)
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Alan Dove
Breaching the barrier
Nature Biotechnology 26, 1213-1215 (2008)
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C Kramer & P Gedeck
Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors
J Chem Inf Model, 51, 707-720 (2011)
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M Habgood & SL Price
Isomers, Conformers, and Cocrystal Stoichiometry: Insights from the Crystal Energy Landscapes of Caffeine with the Hydroxybenzoic Acids
Crystal Growth & Design, 10, 3263-3272 (2010)
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P.J. Ballester & J.B.O. Mitchell
Comments on "Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets": Significance for the Validation of Scoring Functions
Journal of Chemical Information and Modeling, 51, 1739-1741 (2011)
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R. Lowe, H.Y. Mussa, J.B.O. Mitchell & R.C. Glen
Classifying Molecules Using a Sparse Probabilistic Kernel Binary Classifier
Journal of Chemical Information and Modeling, 51, 1539-1544 (2011)
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T. C. Havens, J. C. Bezdek, J. M. Keller, M. Popescu
Dunn's cluster validity index as a contrast measure of VAT images
In Pattern Recognition, 2008. ICPR 2008. 19th International Conference on (December 2008), pp. 1-4.
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Julia Handl, Joshua Knowles, Douglas B. Kell
Computational cluster validation in post-genomic data analysis
Bioinformatics, 21, 3201-3212 (2005)
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Johannes Kastner
Umbrella sampling
WIREs Computational Molecular Science, 1, 932-942 (2011)
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Ignacio Soteras, Modesto Orozco, F. Javier Luque
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies
J Comput Aided Mol Des, 24, 281-291 (2010)
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German L. Perlovich, Tatyana V. Volkova, Annette Bauer-Brandl
Towards an understanding of the molecular mechanism of solvation of drug molecules: A thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by paracetamol, acetanilide, and phenacetin
J. Pharm. Sci., 95, 2158-2169 (2006)
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Lazaros Mavridis, Brian D. Hudson, and David W. Ritchie
Toward High Throughput 3D Virtual Screening Using Spherical Harmonic Surface Representations
J. Chem. Inf. Model., 47, 1787-1796 (2007)
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Jason H. Steffen
Optimal boarding method for airline passengers
Journal of Air Transport Management, 14, 146-150 (2008)
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M. Svard and A. C. Rasmuson
Structural and energetic aspects of the differences between real and predicted polymorphs
Cryst. Res. Technol. 45, 867-878 (2010)
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Valentin Georgiev, Tomasz Borowski, Margareta Blomberg, Per Siegbahn
A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese
Journal of Biological Inorganic Chemistry, 13, 929-940 (2008)
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Yen Low, Takeki Uehara, Yohsuke Minowa, Hiroshi Yamada, Yasuo Ohno, Tetsuro Urushidani, Alexander Sedykh, Eugene Muratov, Viktor Kuz'min, Denis Fourches, Hao Zhu, Ivan Rusyn, Alexander Tropsha
Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches
Chemical Research in Toxicology, 24, 1251-1262 (2011)
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Thomas Hartung
Toxicology for the twenty-first century
Nature, 460, 208-212 (2009)
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Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed A. Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies
Nucleic Acids Research, 40, D776-D782 (2012)
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Agnieszka Szarecka, Kimberly R. Lesnock, Carlos A. Ramirez-Mondragon, Hugh B. Nicholas, Troy Wymore
The Class D beta-lactamase family: residues governing the maintenance and diversity of function
Protein Engineering, Design & Selection, 24, 801-809 (2011)
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Jason Raymond and Daniel Segre
The Effect of Oxygen on Biochemical Networks and the Evolution of Complex Life
Science, 311, 1764-1767 (2006)
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Mark H. P. Verheij, Chris de Graaf, Gerdien E. de Kloe, Saskia Nijmeijer, Henry F. Vischer, Rogier A. Smits, Obbe P. Zuiderveld, Saskia Hulscher, Linda Silvestri, Andrew J. Thompson, Jacqueline E. van Muijlwijk-Koezen, Sarah C. R. Lummis, Rob Leurs, Iwan J. P. de Esch
Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H4 and the ion channel serotonin 5-HT3A
Bioorganic & Medicinal Chemistry Letters, 21, 5460-5464 (2011)
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Firas Khatib, Frank DiMaio, Seth Cooper, Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zabranska, Iva Pichova, James Thompson, Zoran Popovic, Mariusz Jaskolski, David Baker
Crystal structure of a monomeric retroviral protease solved by protein folding game players
Nat Struct Mol Biol, 18, 1175-1177 (2011)
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R. Lowe, H.Y. Mussa, F. Nigsch, R.C. Glen & J.B.O. Mitchell
Predicting the mechanism of phospholipidosis
Journal of Cheminformatics, 4:2 (2012)
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Andrew R. Leach, Michael M. Hann
Molecular complexity and fragment-based drug discovery: ten years on
Current Opinion in Chemical Biology, 15, 489-496 (2011)
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Neil D. Rawlings, Alan J. Barrett, Alex Bateman
Asparagine Peptide Lyases
Journal of Biological Chemistry, 286, 38321-38328 (2011)
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Gianpiero Garau, Anne M. Di Guilmi, Barry G. Hall
Structure-Based Phylogeny of the Metallo-beta-Lactamases
Antimicrobial Agents and Chemotherapy, 49, 2778-2784 (2005)
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Isabelle Krimm, Jean-Marc Lancelin, and Jean-Pierre Praly
Binding Evaluation of Fragment-Based Scaffolds for Probing Allosteric Enzymes
Journal of Medicinal Chemistry, 55, 1287-1295 (2012)
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Michael J. Keiser, Vincent Setola, John J. Irwin, Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jerome Hert, Kelan L. Thomas, Douglas D. Edwards, Brian K. Shoichet, Bryan L. Roth
Predicting new molecular targets for known drugs
Nature, 462, 175-181 (2009)
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Moritz Schutte, Alexander Skupin, Daniel Segre, Oliver Ebenhoeh
Modeling the complex dynamics of enzyme-pathway coevolution
Chaos: An Interdisciplinary Journal of Nonlinear Science, 20, 045115 (2010)
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Astikainen, K., Holm, L., Pitkanen, E., Szedmak, S. & Rousu, J.
Towards structured output prediction of enzyme function.
BMC Proceedings 2:S2 (2008)
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Shoshana D Brown, John A Gerlt, Jennifer L Seffernick and Patricia C Babbitt
A gold standard set of mechanistically diverse enzyme superfamilies
Genome Biology, 7:R8 (2006)
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Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
PLoS Comput Biol 5: e1000605 (2009)
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Minglei Wang, Liudmila S. Yafremava, Derek Caetano-Anolles, Jay E. Mittenthal, Gustavo Caetano-Anolles
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world.
Genome research, 17, 1572-1585 (2007)
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Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies
PLoS Comput Biol, 8:e1002403 (2012)
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N. Nath & J.B.O. Mitchell
Is EC class predictable from reaction mechanism?
BMC Bioinformatics, 13:60 (2012)
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Luna De Ferrari, Stuart Aitken, Jano van Hemert and Igor Goryanin
EnzML: Multi-label prediction of enzyme classes using InterPro signatures
BMC Bioinformatics, 13:61 (2012)
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Michael Buhl, Tanja van Mourik
NMR spectroscopy: quantum-chemical calculations
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Thomas Hamelryck, Mikael Borg, Martin Paluszewski, Jonas Paulsen, Jes Frellsen, Christian Andreetta, Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg
Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized
PLoS ONE, 5:e13714 (2010)
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Svetlana Bureeva, Yuri Nikolsky
Quantitative knowledge-based analysis in compound safety assessment.
Expert Opinion on Drug Metabolism & Toxicology, 7, 287-298 (2011)
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Laurence Leherte, Daniel P. Vercauteren
Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models
Journal of Computer-Aided Molecular Design, 25, 913-930 (2011)
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Hans M. Senn, David O'Hagan, Walter Thiel
Insight into Enzymatic C-F Bond Formation from QM and QM/MM Calculations
Journal of the American Chemical Society, 127, 13643-13655 (2005)
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A. P. Harding, P. L. A. Popelier
pKa Prediction from an ab initio bond length: part 2-phenols
Phys. Chem. Chem. Phys., 13, 11264-11282 (2011)
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A. P. Harding, P. L. A. Popelier
pKa prediction from an ab initio bond length: part 3--benzoic acids and anilines.
Physical chemistry chemical physics : PCCP, 13, 11283-11293 (2011)
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Lakshmi Y. S. Narasimham, Vasant D. Barhate
Kinetic and intrinsic solubility determination of some beta-blockers and antidiabetics by potentiometry
Journal of Pharmacy Research, 4, 532-536 (2011)
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Natasha Latysheva, Vivien L. Junker, William J. Palmer, Geoffrey A. Codd, Daniel Barker
The evolution of nitrogen fixation in cyanobacteria
Bioinformatics, 28, 603-606 (2012)
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Barry G Hall, Stephen J Salipante, Miriam Barlow
Independent Origins of Subgroup Bl+B2 and Subgroup B3 Metallo-beta-Lactamases
Journal of Molecular Evolution, 59, 133-141 (2004)
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Kyung Mo Kim, Gustavo Caetano-Anolles
Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data.
Molecular Biology and Evolution, 27, 1710-1733 (2010)
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Michael J. Schnieders, Jonas Baltrusaitis, Yue Shi, Gaurav Chattree, Lianqing Zheng, Wei Yang, Pengyu Ren
The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field
J. Chem. Theory Comput. 8, 1721-1736 (2012)
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Minglei Wang, Ying-Ying Jiang, Kyung Mo Kim, Ge Qu, Hong-Fang Ji, Jay E. Mittenthal, Hong-Yu Zhang, and Gustavo Caetano-Anolles
A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation
Mol. Biol. Evol., 28, 567-582 (2011)
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Victor E. Kuz'min, Pavel G. Polishchuk, Anatoly G. Artemenko, Sergey A. Andronati
Interpretation of QSAR Models Based on Random Forest Methods
Mol. Inf., 30, 593-603 (2011)
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HH Lin, LY Han, HL Zhang, CJ Zheng, B Xie, ZW Cao and YZ Chen
Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach
BMC Bioinformatics 7:S13 (2006)
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Lourdes Cucurull-Sanchez
Successful identification of key chemical structure modifications that lead to improved ADME profiles
Journal of Computer-Aided Molecular Design, 24, 449-458 (2010)
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Nidhi, Meir Glick, John W. Davies, Jeremy L. Jenkins
Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases
Journal of Chemical Information and Modeling, 46, 1124-1133 (2006)
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Richard Pollard
Home Advantage in Football: A Current Review of an Unsolved Puzzle
The Open Sports Sciences Journal, 1, 12-14 (2008)
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Arren Bar-Even, Elad Noor, Yonatan Savir, Wolfram Liebermeister, Dan Davidi, Dan S. Tawfik, Ron Milo
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters
Biochemistry, 50, 4402-4410 (2011)
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Claes R. Andersson, Mats G. Gustafsson, Helena Strombergsson
Quantitative chemogenomics: machine-learning models of protein-ligand interaction.
Current Topics in Medicinal Chemistry, 11, 1978-1993 (2011)
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Bernhard Baum, Laveena Muley, Michael Smolinski, Andreas Heine, David Hangauer and Gerhard Klebe
Non-additivity of Functional Group Contributions in Protein-Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry
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Tjelvar S. G. Olsson, Mark A. Williams, William R. Pitt and John E. Ladbury
The thermodynamics of protein-ligand interaction and solvation: Insights for ligand design
J Mol Biol, 384, 1002-1017 (2008)
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Juan C Trivino & Florencio Pazos
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds
BMC Systems Biology, 4:46 (2010)
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Chenzhong Liao, Markus Sitzmann, Angelo Pugliese, Marc C. Nicklaus
Software and resources for computational medicinal chemistry.
Future Medicinal Chemistry, 3, 1057-1085 (2011)
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DS Palmer, JL McDonagh, JBO Mitchell, T van Mourik & MV Fedorov
First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules
J Chem Theory Comput, 8, 3322-3337 (2012)
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Eugen Lounkine, Michael J. Keiser, Steven Whitebread, Dmitri Mikhailov, Jacques Hamon, Jeremy L. Jenkins, Paul Lavan, Eckhard Weber, Allison K. Doak, Serge Cote, Brian K. Shoichet, Laszlo Urban
Large-scale prediction and testing of drug activity on side-effect targets
Nature, 486, 361-367 (2012)
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A. Donev, I. Cisse, D. Sachs, E. Variano, F. H. Stillinger, R. Connelly, S. Torquato, P. M. Chaikin
Improving the density of jammed disordered packings using ellipsoids
Science, 303, 990-993 (2004)
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Aurelien de la Lande, Dennis Salahub, Vicent Moliner, Helene Gerard, Jean-Philip Piquemal and Olivier Parisel
Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their CuM Coordination Sphere
Inorg. Chem., 48, 7003-7005 (2009)
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Bruce F. Milne, Miguel A. L. Marques and Fernando Nogueira
Fragment molecular orbital investigation of the role of AMP protonation in firefly luciferase pH-sensitivity
Phys. Chem. Chem. Phys., 12, 14285-14293 (2010)
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B. Karasulu, O. Keskin, B. Erman
Reaction path analysis for demethylation process of histone tail lysine residues
5th International Symposium on Health Informatics and Bioinformatics (HIBIT), Antalya pp 197-205 (2010)
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Christos A. Ouzounis
Rise and Demise of Bioinformatics? Promise and Progress
PLoS Comput Biol, 8, e1002487 (2012)
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P.J. Ballester, M. Mangold, N.I. Howard, R.L. Marchese Robinson, C. Abell, J. Blumberger & J.B.O. Mitchell
Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
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Slavica Eric, Marko Kalinic, Aleksandar Popovic, Mire Zloh, Igor Kuzmanovski
Prediction of aqueous solubility of drug-like molecules using a novel algorithm for automatic adjustment of relative importance of descriptors implemented in counter-propagation artificial neural networks
International Journal of Pharmaceutics, 437, 232-241 (2012)
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BSW Chang, JA Ugalde, MV Matz
Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins
Methods in Enzymology, 395, 652-670 (2005)
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R. Otto, J. Brox, S. Trippel, M. Stei, T. Best, R. Wester
Single solvent molecules can affect the dynamics of substitution reactions
Nature Chem, 4, 534-538 (2012)
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Qiang Zhu, Artem R. Oganov, Colin W. Glass, Harold T. Stokes
Constrained evolutionary algorithm for structure prediction of molecular crystals: methodology and applications
Acta Crystallographica Section B, 68, 215-226 (2012)
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David A. Bardwell, Claire S. Adjiman, Yelena A. Arnautova, Ekaterina Bartashevich, Stephan X. M. Boerrigter, Doris E. Braun, Aurora J. Cruz Cabeza, Graeme M. Day, Raffaele G. Della Valle,
Gautam R. Desiraju, Bouke P. van Eijck, Julio C. Facelli, Marta B. Ferraro, Damian Grillo, Matthew Habgood, Detlef W. M. Hofmann, Fridolin Hofmann, K. V. Jovan Jose,
Panagiotis G. Karamertzanis, Andrei V. Kazantsev, John Kendrick, Liudmila N. Kuleshova, Frank J. J. Leusen, Andrey V. Maleev, Alston J. Misquitta, Sharmarke Mohamed, Richard J. Needs,
Marcus A. Neumann, Denis Nikylov, Anita M. Orendt, Rumpa Pal, Constantinos C. Pantelides, Chris J. Pickard, Louise S. Price, Sarah L. Price, Harold A. Scheraga, Jacco van de Streek,
Tejender S. Thakur, Siddharth Tiwari, Elisabetta Venuti, Ilia K. Zhitkov
Towards crystal structure prediction of complex organic compounds -- a report on the fifth blind test
Acta Crystallographica Section B, 67, 535-551 (Dec 2011)
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Noel O'Boyle
Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI
Journal of Cheminformatics, 4, 22 (2012)
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Bin Chen, David Wild, Rajarshi Guha
PubChem as a Source of Polypharmacology
J. Chem. Inf. Model. In Journal of Chemical Information and Modeling, 49, 2044-2055 (2009)
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Barry G. Hall, Andreas Pikis, John Thompson
Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations.
Molecular Biology and Evolution, 26, 2487-2497 (2009)
https://doi.org/10.1093/molbev/msp162
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Alison Cuff, Oliver Redfern, Benoit Dessailly, Christine Orengo
Exploiting Protein Structures to Predict Protein Functions
Protein Function Prediction for Omics Era, 107-123 (2011) (edited by: Daisuke Kihara)
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R.G Alderson, L. De Ferrari, L. Mavridis, J.L. McDonagh, J.B.O. Mitchell & N. Nath
Enzyme Informatics
Current Topics in Medicinal Chemistry, 12, 1911-1923 (2012)
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Elin Teppa, Angela D. Wilkins, Morten Nielsen, Cristina Marino Buslje
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
BMC Bioinformatics, 13, 235 (2012)
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Cristian R. Munteanu, Humberto Gonzalez-Diaz, Alexandre L. Magalhaes
Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices
Journal of Theoretical Biology, 254, 476-482 (2008)
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Jeremy L. Jenkins, Andreas Bender, John W. Davies
In silico target fishing: Predicting biological targets from chemical structure
Drug Discovery Today: Technologies, 3, 413-421 (2006)
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Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu, Ying Ding, David Wild
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data
BMC Bioinformatics, 11, 255 (2010)
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Sonny K. Kjaerulff, Louis Wich, Jens Kringelum, Ulrik P. Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Soren Brunak, Tudor I. Oprea, Olivier Taboureau
ChemProt-2.0: visual navigation in a disease chemical biology database
Nucleic Acids Research, 41, D464-D469 (2013)
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Karin Voordeckers, Chris A. Brown, Kevin Vanneste, Elisa van der Zande, Arnout Voet, Steven Maere, Kevin J. Verstrepen
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
PLoS Biol, 10, e1001446 (2012)
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Tony Freeth, Alexander Jones, John M. Steele, Yanis Bitsakis
Calendars with Olympiad display and eclipse prediction on the Antikythera Mechanism
Nature, 454, 614-617 (2008)
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Daniel J. Sindhikara, Norio Yoshida, Fumio Hirata
Placevent: An algorithm for prediction of explicit solvent atom distribution - Application to HIV-1 protease and F-ATP synthase
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Takashi Imai, Koji Oda, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design
J. Am. Chem. Soc., 131, 12430-12440 (2009)
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Martin C. Stumpe, Nikolay Blinov, David Wishart, Andriy Kovalenko, Vijay S. Pande
Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation
J. Phys. Chem. B, 115, 319-328 (2010)
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Janet Newman, Olan Dolezal, Vincent Fazio, Tom Caradoc-Davies, Thomas S. Peat
The DINGO dataset: a comprehensive set of data for the SAMPL challenge.
Journal of Computer-Aided Molecular Design, 26, 497-503 (2012)
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S. Whelan, N. Goldman
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
Molecular Biology and Evolution, 18, 691-699 (2001)
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Alston J. Misquitta, Gareth W. A. Welch, Anthony J. Stone, Sarah L. Price
A first principles prediction of the crystal structure of C6Br2ClFH2
Chemical Physics Letters, 456, 105-109 (2008)
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Gregory A Petsko
Seek and ye shall maybe find
Genome Biology, 1:comment1005-comment1005.2 (2000)
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Si Q. Le, Olivier Gascuel
An Improved General Amino Acid Replacement Matrix
Molecular Biology and Evolution, 25, 1307-1320 (2008)
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Richard Edwards, Denis Shields
GASP: Gapped Ancestral Sequence Prediction for proteins
BMC Bioinformatics, 5, 123 (2004)
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Simon Gane, Dimitris Georganakis, Klio Maniati, Manolis Vamvakias, Nikitas Ragoussis, Efthimios M. C. Skoulakis, Luca Turin
Molecular Vibration-Sensing Component in Human Olfaction
PLoS ONE, 8, e55780 (2013)
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Christopher B. Eiben, Justin B. Siegel, Jacob B. Bale, Seth Cooper, Firas Khatib, Betty W. Shen, Foldit Players, Barry L. Stoddard, Zoran Popovic, David Baker
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.
Nature Biotechnology, 30, 190-192 (2012)
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Sam Mavandadi, Stoyan Dimitrov, Steve Feng, Frank Yu, Uzair Sikora, Oguzhan Yaglidere, Swati Padmanabhan, Karin Nielsen, Aydogan Ozcan
Distributed Medical Image Analysis and Diagnosis through Crowd-Sourced Games: A Malaria Case Study
PLoS ONE, 7, e37245 (2012)
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Alexander Kawrykow, Gary Roumanis, Alfred Kam, Daniel Kwak, Clarence Leung, Chu Wu, Eleyine Zarour, Phylo players, Luis Sarmenta, Mathieu Blanchette, Jerome Waldispuhl
Phylo: a citizen science approach for improving multiple sequence alignment.
PLoS ONE, 7, e31362 (2012)
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Qian-Nan Hu, Hui Zhu, Xiaobing Li, Manman Zhang, Zhe Deng, Xiaoyan Yang, Zixin Deng
Assignment of EC Numbers to Enzymatic Reactions with Reaction Difference Fingerprints
PLoS ONE, 7, e52901 (2012)
https://doi.org/10.1371/journal.pone.0052901
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Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovic, Foldit Players
Predicting protein structures with a multiplayer online game
Nature, 466, 756-760, (2010)
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Burak Erman
Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations.
Physical Biology, 8, 056003 (2011)
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Alejandro Panjkovich, Xavier Daura
Exploiting protein flexibility to predict the location of allosteric sites
BMC Bioinformatics, 13, 273 (2012)
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Barry G. Hall, Miriam Barlow
Revised Ambler classification of beta-lactamases
Journal of Antimicrobial Chemotherapy, 55, 1050-1051 (2005)
https://doi.org/10.1093/jac/dki130
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Z. Wang, W. Fast, A. M. Valentine, S. J. Benkovic
Metallo-beta-lactamase: structure and mechanism.
Current Opinion in Chemical Biology, 3, 614-622 (1999)
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Maryam Salahinejad, Tu C. Le, David A. Winkler
Capturing the crystal: prediction of enthalpy of sublimation, crystal lattice energy, and melting points of organic compounds.
Journal of Chemical Information and Modeling, 53, 223-229 (2013)
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Syed A. Bukhari, Gustavo Caetano-Anolles
Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes
PLoS Comput Biol, 9, e1003009 (2013)
https://doi.org/10.1371/journal.pcbi.1003009
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Fabio Simona, Alessandra Magistrato, Matteo D. Peraro, Andrea Cavalli, Alejandro J. Vila, Paolo Carloni
Common Mechanistic Features among Metallo-beta-lactamases
Journal of Biological Chemistry, 284, 28164-28171 (2009)
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Dingguo Xu, Hua Guo, Qiang Cui
Antibiotic Deactivation by a Dizinc beta-Lactamase: Mechanistic Insights from QM/MM and DFT Studies
J. Am. Chem. Soc., 129, 10814-10822 (2007)
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Hanna-Kirsti K. Leiros, Pardha S. Borra, Bjorn Olav O. Brandsdal, Kine Susann Waade S. Edvardsen, James Spencer, Timothy R. Walsh, Orjan Samuelsen
Crystal structure of the mobile metallo-beta-lactamase AIM-1 from Pseudomonas aeruginosa: insights into antibiotic binding and the role of Gln157.
Antimicrobial Agents and Chemotherapy, 56, 4341-4353 (2012)
https://doi.org/10.1128/aac.00448-12
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James Spencer, Jonathan Read, Richard B. Sessions, Steven Howell, G. Michael Blackburn, Steven J. Gamblin
Antibiotic Recognition by Binuclear Metallo-beta-Lactamases Revealed by X-ray Crystallography
J. Am. Chem. Soc., 127, 14439-14444 (2005)
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Yoshihiro Yamaguchi, Takahiro Kuroki, Hisami Yasuzawa, Toshihiro Higashi, Wanchun Jin, Akiko Kawanami, Yuriko Yamagata, Yoshichika Arakawa, Masafumi Goto, Hiromasa Kurosaki
Probing the role of Asp-120(81) of metallo-beta-lactamase (IMP-1) by site-directed mutagenesis, kinetic studies, and X-ray crystallography.
Journal of Biological Chemistry, 280, 20824-20832 (2005)
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HongMin Zhang, Quan Hao
Crystal structure of NDM-1 reveals a common beta-lactam hydrolysis mechanism
The FASEB Journal, 25, 2574-2582 (2011)
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Claude Grasland, France Guerin-Pace, Marion Le Texier & Benedicte Garnier
Diffusion of foreign euro coins in France, 2002-2012
Population and Societies 488 (2012) Institut National d'Etudes Demographiques (INED)
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L. Mavridis & J.B.O. Mitchell
Predicting the protein targets for athletic performance-enhancing substances
Journal of Cheminformatics, 5:31 (2013)
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L. Mavridis, N. Nath & J.B.O. Mitchell
PFClust: a novel parameter free clustering algorithm
BMC Bioinformatics, 14:213 (2013)
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Anthony M. Reilly, Alexandre Tkatchenko
Seamless and Accurate Modeling of Organic Molecular Materials
J. Phys. Chem. Lett., 4, 1028-1033 (2013)
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Tiddo J. Mooibroek, Patrick Gamez
Halogen bonding versus hydrogen bonding: what does the Cambridge Database reveal?
CrystEngComm 15, 4565-4570 (2013)
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A. Koutsoukas, R. Lowe, Y. KalantarMotamedi, H. Y. Mussa, W. Klaffke, J. B. O. Mitchell, R. C. Glen & A. Bender
In silico target predictions: defining a benchmarking dataset and comparison of performance of the multiclass Naive Bayes and Parzen-Rosenblatt Window
J. Chem. Inf. Model. 53, 1957-1966 (2013)
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Alessandro Lusci, Gianluca Pollastri, Pierre Baldi
Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules
J. Chem. Inf. Model. 53, 1563-1575 (2013)
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Daniel Barker, David Ferrier, Peter Holland, John B. O. Mitchell, Heleen Plaisier, Michael Ritchie, Steven Smart
4273pi: Bioinformatics education on low cost ARM hardware
BMC Bioinformatics, 14:243 (2013)
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Bruno Louis, Vijay K. Agrawal, Padmakar V. Khadikar
Prediction of intrinsic solubility of generic drugs using MLR, ANN and SVM analyses
European Journal of Medicinal Chemistry, 45, 4018-4025 (2010)
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C. Mackay, M. Davies, V. Summerfield, and G. Maxwell
From pathways to people: applying the adverse outcome pathway (AOP) for skin sensitization to risk assessment
ALTEX, Jun. 2013.
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Hamse Y Mussa, John BO Mitchell and Robert C Glen
Full "Laplacianised" posterior naive Bayesian algorithm
Journal of Cheminformatics 5:37 (2013)
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Adam Fedorowicz, Lingyi Zheng, Harshinder Singh, Eugene Demchuk
QSAR Study of Skin Sensitization Using Local Lymph Node Assay Data
International Journal of Molecular Sciences, 5, 56-66 (2004)
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D. W. Roberts and G. Y. Patlewicz
Updating the skin sensitization in vitro data assessment paradigm in 2009 - a chemistry and QSAR perspective
J. Appl. Toxicol., 30, 286-288 (2010)
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M. Hewitt, M. T. D. Cronin, S. J. Enoch, J. C. Madden, D. W. Roberts, J. C. Dearden
In Silico Prediction of Aqueous Solubility: The Solubility Challenge
J. Chem. Inf. Model., 49, 2572-2587 (2009)
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Sharath Golla, Sundar Madihally, Robert L. Robinson, Khaled A. M. Gasem
Quantitative structure-property relationship modeling of skin sensitization: A quantitative prediction
Toxicology in Vitro, 23, 454-465 (2009)
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Julia D. Fischer, Gemma L. Holliday, Syed A. Rahman, Janet M. Thornton
The structures and physicochemical properties of organic cofactors in biocatalysis
Journal of Molecular Biology, 403, 803-824 (2010)
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David Talavera, Roman A. Laskowski, Janet M. Thornton
WSsas: a web service for the annotation of functional residues through structural homologues
Bioinformatics, 25, 1192-1194 (2009)
https://doi.org/10.1093/bioinformatics/btp116
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Antonio del Sol, Chung-Jung Tsai, Buyong Ma, Ruth Nussinov
The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways
Structure, 17, 1042-1050 (2009)
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Ariel E. Baya, Pablo M. Granitto
How Many Clusters: A Validation Index for Arbitrary-Shaped Clusters
IEEE/ACM Trans. Comput. Biol. Bioinformatics, 10, 401-414 (2013)
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Hee Shin S. Kim, Jay E. Mittenthal, Gustavo Caetano-Anolles
Widespread Recruitment of Ancient Domain Structures in Modern Enzymes during Metabolic Evolution.
Journal of Integrative Bioinformatics, 10:214 (2013)
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William M. Brandler, Andrew P. Morris, David M. Evans, Thomas S. Scerri, John P. Kemp, Nicholas J. Timpson, Beate St Pourcain, George D. Smith, Susan M. Ring, John Stein, Anthony P. Monaco, Joel B. Talcott, Simon E. Fisher, Caleb Webber, Silvia Paracchini
Common Variants in Left/Right Asymmetry Genes and Pathways Are Associated with Relative Hand Skill
PLoS Genet, 9, e1003751 (2013)
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John Bohannon
Who's Afraid of Peer Review?
Science, 342, No. 6154, 60-65 (2013)
https://doi.org/10.1126/science.342.6154.60
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Shivas R. Amin, Serkan Erdin, R. Matthew Ward, Rhonald C. Lua, Olivier Lichtarge
Prediction and experimental validation of enzyme substrate specificity in protein structures
Proceedings of the National Academy of Sciences (2013), 201305162,
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Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff Macintyre, Tomas Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost
ISCB Computational Biology Wikipedia Competition
PLoS Comput Biol, 9, e1003242 (2013)
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Armen Y. Mulkidjanian, Michael Y. Galperin
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
Biology Direct, 4:27 (2009)
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Bin Lin, Ka-Yiu Wong, Char Hu, Hironori Kokubo, B. Montgomery Pettitt
Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions
J. Phys. Chem. Lett. 2, 1626-1632 (2011)
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Alister McGrath
Has Science Eliminated God? Richard Dawkins and the Meaning of Life
Science & Christian Belief, 17, 117-135 (2005)
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Michael Poole
A Critique of Aspects of the Philosophy and Theology of Richard Dawkins
Science & Christian Belief, 6, 41-59 (1994)
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K. Musayeva, T. Henderson, J.B.O. Mitchell & L. Mavridis
PFClust: an optimised implementation of a parameter-free clustering algorithm
Source Code for Biology and Medicine, 9:5 (2014)
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J.B.O. Mitchell
Machine learning methods in chemoinformatics
WIREs Comput. Mol. Sci., 4, 468-481 (2014)
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J.L. McDonagh, N. Nath, L. De Ferrari, T. van Mourik & J.B.O. Mitchell
Uniting Cheminformatics and Chemical Theory to Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules
J. Chem. Inf. Model., 54, 844-856 (2014)
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Aboul E. Hassanien, Eiman T. Al-Shammari, Neveen I. Ghali
Computational intelligence techniques in bioinformatics
Computational Biology and Chemistry, 47, 37-47 (2013)
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Jean-Francois Truchon, B. Montgomery Pettitt, Paul Labute
A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
J. Chem. Theory Comput. 10, 934-941 (2014)
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Salahinejad, M., Le, T. C. & Winkler, D. A.
Aqueous solubility prediction: Do crystal lattice interactions help?
Mol. Pharmaceutics 10, 2757-2766 (2013)
https://doi.org/10.1021/mp4001958
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Awwadi, F. F., Haddad, S. F., Twamley, B. & Willett, R. D.
Effect of intermolecular interactions on the molecular structure; theoretical study and crystal structures of 4-bromopyridinium tetrafluoroborate and diaqua(3-bromopyridine)difluorocopper(ii)
CrystEngComm 14, 6761-6769 (2012)
https://doi.org/10.1039/c2ce25433f
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Perlovich, G. L.
Thermodynamic approaches to the challenges of solubility in drug discovery and development
Mol. Pharmaceutics 11, 1-11 (2013)
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M. A. Hicks, A. E. Barber, L.-A. A. Giddings, J. Caldwell, S. E. O'Connor, and P. C. Babbitt,
The evolution of function in strictosidine synthase-like proteins
Proteins, 79, 3082-3098 (2011)
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G. J. P. van Westen, A. Gaulton, and J. P. Overington,
Chemical, target, and bioactive properties of allosteric modulation
PLoS Comput Biol, 10, e1003559 (2014)
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J. Comer, S. Judge, D. Matthews, L. Towers, B. Falcone, J. Goodman, and J. Dearden,
The intrinsic aqueous solubility of indomethacin,
ADMET & DMPK, 2, 18-32 (2014)
https://doi.org/10.5599/admet.2.1.33
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L. De Ferrari & J.B.O. Mitchell
From sequence to enzyme mechanism using multi-label machine learning
BMC Bioinformatics, 15:150 (2014)
https://doi.org/10.1186/1471-2105-15-150
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N. Nath, J.B.O. Mitchell & G. Caetano-Anolles
The Natural History of Biocatalytic Mechanisms
PLoS Computational Biology, 10, e1003642 (2014)
https://doi.org/10.1371/journal.pcbi.1003642
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D.S. Palmer & J.B.O. Mitchell
Is Experimental Data Quality the Limiting Factor in Predicting the Aqueous Solubility of Druglike Molecules?
Molecular Pharmaceutics, 11, 2962-2972 (2014)
https://doi.org/10.1021/mp500103r
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M. D. Brazas, F. Lewitter, M. V. Schneider, C. W. G. van Gelder, and P. M. Palagi
A quick guide to genomics and bioinformatics training for clinical and public audiences
PLoS Comput Biol, 10, e1003510 (2014)
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Didier Mathieu
Simple Alternative to Neural Networks for Predicting Sublimation Enthalpies from Fragment Contributions
Ind. Eng. Chem. Res., 51, 2814-2819 (2012)
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Jose A. Santos, Houssam Nassif, David Page, Stephen Muggleton, Michael E. Sternberg
Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study
BMC Bioinformatics, 13:162 (2012)
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Pulan Yu, David J. Wild
Fast rule-based bioactivity prediction using associative classification mining.
Journal of Cheminformatics, 4:29 (2012)
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Francesco Napolitano, Yan Zhao, Vania Moreira, Roberto Tagliaferri, Juha Kere, Mauro D'Amato, Dario Greco
Drug repositioning: a machine-learning approach through data integration
Journal of Cheminformatics, 5:30 (2013)
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Eshel Faraggi, Andrzej Kloczkowski
A global machine learning based scoring function for protein structure prediction
Proteins, 82, 752-759 (2014)
https://doi.org/10.1002/prot.24454
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Saket Navlakha, Xin He, Christos Faloutsos, Ziv Bar-Joseph
Topological properties of robust biological and computational networks
Journal of The Royal Society Interface, 11, 20140283 (2014)
https://doi.org/10.1098/rsif.2014.0283
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Nicholas Furnham, Gemma L. Holliday, Tjaart A. de Beer, Julius O. Jacobsen, William R. Pearson, Janet M. Thornton
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes
Nucleic Acids Research, 42, D485-D489 (2014)
https://doi.org/10.1093/nar/gkt1243
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Brett Hanson, Charles Westin, Mario Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L. MacDonald, Greg Dodge, Paule M. Boli, Cyprian W. Corwin, Haeja Kessler, Talia McKay, Herbert J. Bernstein, Paul A. Craig
Estimation of protein function using template-based alignment of enzyme active sites
BMC Bioinformatics, 15:87 (2014)
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Jerome P. Nilmeier, Daniel A. Kirshner, Sergio E. Wong, Felice C. Lightstone
Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure
PLoS ONE 8:e62535 (2013)
https://doi.org/10.1371/journal.pone.0062535
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Hao Fan, Daniel S. Hitchcock, Ronald D. Seidel, Brandan Hillerich, Henry Lin, Steven C. Almo, Andrej Sali, Brian K. Shoichet, Frank M. Raushel
Assignment of Pterin Deaminase Activity to an Enzyme of Unknown Function Guided by Homology Modeling and Docking
Journal of the American Chemical Society, 135, 795-803 (2012)
https://doi.org/10.1021/ja309680b
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Vladimir Chupakhin, Gilles Marcou, Igor Baskin, Alexandre Varnek, Didier Rognan
Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints
J. Chem. Inf. Model., 53, 763-772 (2013)
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Ya-Wen Hsiao, Urban Fagerholm, Ulf Norinder
In Silico Categorization of in Vivo Intrinsic Clearance Using Machine Learning
Mol. Pharmaceutics, 10, 1318-1321 (2013)
https://doi.org/10.1021/mp300484r
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Yoshihiko Matsuta, Masahiro Ito, Yukako Tohsato
ECOH: an enzyme commission number predictor using mutual information and a support vector machine.
Bioinformatics, 29, 365-372 (2013)
https://doi.org/10.1093/bioinformatics/bts700
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Jooyeon Park, Ian Nessler, Brian McClain, Dainius Macikenas, Jonas Baltrusaitis, Michael J. Schnieders
Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy
J. Chem. Theory Comput., 10, 2781-2791 (2014)
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F. Baier and N. Tokuriki,
Connectivity between catalytic landscapes of the metallo-beta-lactamase superfamily.
Journal of Molecular Biology 426, 2442-2456 (2014)
https://doi.org/10.1016/j.jmb.2014.04.013
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R.G. Alderson, D. Barker & J.B.O. Mitchell,
One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees
Journal of Molecular Evolution, 79, 117-129 (2014)
https://doi.org/10.1007/s00239-014-9639-7
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K. Nikolic, L. Mavridis, O.M. Bautista-Aguilera, J. Marco-Contelles, H. Stark, M. do Carmo Carreiras, I. Rossi, P. Massarelli, D. Agbaba, R.R. Ramsay, J.B.O. Mitchell
Predicting targets of compounds against neurological diseases using cheminformatic methodology
Journal of Computer-Aided Molecular Design, 29, 183-198 (2015)
https://doi.org/10.1007/s10822-014-9816-1
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R.E. Skyner, J.L. McDonagh, C.R. Groom, T. van Mourik & J.B.O. Mitchell,
A Review of Methods for the Calculation of Solution Free Energies and the Modelling of Systems in Solution,
Physical Chemistry Chemical Physics, 17, 6174-6191 (2015)
https://doi.org/10.1039/C5CP00288E
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Kew W, Mitchell JBO
Greedy and Linear Ensembles of Machine Learning Methods Outperform Single Approaches for QSPR Regression Problems
Mol Inf. 34, 634-647 (2015)
https://doi.org/10.1002/minf.201400122
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Rui-Juan Li, Ya-Li Wang, Qing-HeWang, Jian Wang, and Mao-Sheng Cheng,
In Silico Design of Human IMPDH Inhibitors Using Pharmacophore Mapping and Molecular Docking Approaches,
Computational and Mathematical Methods in Medicine, 418767 (2015)
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I. V. Tetko, Y. Sushko, S. Novotarskyi, L. Patiny, I. Kondratov, A. E. Petrenko, L. Charochkina, and A. M. Asiri,
How accurately can we predict the melting points of drug-like compounds?
J. Chem. Inf. Model., vol. 54, no. 12, pp. 3320-3329 (2014)
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M. A. Hamdalla, S. Rajasekaran, D. F. Grant, and I. I. Mandoiu,
Metabolic pathway predictions for metabolomics: a molecular structure matching approach,
J. Chem. Inf. Model., Feb. 2015.
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R. C. Penner, E. S. Andersen, J. L. Jensen, A. K. Kantcheva, M. Bublitz, P. Nissen, A. M. H. Rasmussen, K. L. Svane, B. Hammer, R. Rezazadegan, N. C. Nielsen, J. T. Nielsen, and J. E. Andersen,
Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture,
Nature Communications, vol. 5, article number 5803 (2014)
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J. Alvarsson, M. Eklund, C. Andersson, L. Carlsson, O. Spjuth, and J. E. S. Wikberg,
Benchmarking study of parameter variation when using signature fingerprints together with support vector machines,
J. Chem. Inf. Model., vol. 54, no. 11, pp. 3211-3217, (2014)
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P. Franco,
Orphan drugs: the regulatory environment,
Drug Discovery Today, vol. 18, no. 3-4, pp. 163-172 (2013)
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P. Franco, N. Porta, J. D. Holliday, and P. Willett,
The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation,
Journal of Cheminformatics, vol. 6, no. 1, article number 5 (2014)
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H. Edwards, S. Abeln, and C. M. Deane,
Exploring fold space preferences of new-born and ancient protein superfamilies,
PLoS Comput Biol, vol. 9, no. 11, article number e1003325 (2013)
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O. G. Uzoh, A. J. Cruz-Cabeza, and S. L. Price,
Is the fenamate group a polymorphophore? contrasting the crystal energy landscapes of fenamic and tolfenamic acids,
Crystal Growth & Design, vol. 12, no. 8, pp. 4230-4239 (2012)
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J. Spencer, H. Patel, J. J. Deadman, R. A. Palmer, L. Male, S. J. Coles, O. G. Uzoh, and S. L. Price,
The unexpected but predictable tetrazole packing in flexible 1-benzyl-1H-tetrazole,
CrystEngComm, vol. 14, no. 20, pp. 6441-6446 (2012)
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O. G. Uzoh, P. Galek, and S. L. Price,
Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals,
Phys. Chem. Chem. Phys., 2015
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S. Martinez Cuesta, N. Furnham, S. A. Rahman, I. Sillitoe, and J. M. Thornton,
The evolution of enzyme function in the isomerases,
Current Opinion in Structural Biology, vol. 26, pp. 121-130 (2014)
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K.-H. Liu, M. Tong, S.-T. Xie, and V. T. Yee Ng,
Genetic programming based ensemble system for microarray data classification,
Computational and Mathematical Methods in Medicine, vol. 2015, no. 193406 (2015)
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A. Avdeef,
Anomalous solubility behavior of several acidic drugs,
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Mussa HY, Mitchell JBO, Afzal AM
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