John Mitchell's Group: All Group Publications
Group | John Mitchell | Alumni: Daniel Almonacid | Florian Nigsch | Noel O'Boyle
This is a full list of our publications. It may also contain some publications relating to work done by current or recent group members before joining or after leaving us, but is not exhaustive in this repect.Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function
D.E. Almonacid, E.R. Yera, J.B.O. Mitchell & P.C. Babbitt,
PLoS Computational Biology, accepted for publication
Understanding the functional roles of amino acid residues in enzyme catalysis
G.L. Holliday, J.B.O. Mitchell & J.M. Thornton
Journal of Molecular Biology, 390, 560-577 (2009)
doi: 10.1016/j.jmb.2009.05.015
PMID 19447117
Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase,
L.M. Blomberg, M. Mangold, J.B.O. Mitchell & J. Blumberger,
J. Chem. Theory Comput., 5, 1284-1294 (2009)
doi: 10.1021/ct800480d
Computational Toxicology: An Overview of the Sources of Data and of Modelling Methods,
F. Nigsch, N.J.M. Macaluso, J.B.O. Mitchell & D. Zmuidinavicius,
Expert Opinion on Drug Metabolism and Toxicology, 5, 1-14 (2009)
doi: 10.1517/17425250802660467
PMID 19236225
Simultaneous Feature Selection and Parameter Optimisation using an Artificial Ant Colony: Case Study of Melting Point Prediction,
N.M. O'Boyle, D.S. Palmer, F. Nigsch & J.B.O. Mitchell,
Chemistry Central Journal, 2:21 (2008)
doi: 10.1186/1752-153X-2-21
PMID 18959785
Ligand-Target Prediction using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics
F. Nigsch, A. Bender, J. L. Jenkins & J.B.O. Mitchell
Journal of Chemical Information and Modeling, 48, 2313-2325 (2008)
doi: 10.1021/ci800079x
PMID 19055411
Toxicological Relationships Between Proteins Obtained from Protein Target Predictions of Large Toxicity Databases
F. Nigsch & J.B.O. Mitchell
Toxicology and Applied Pharmacology, 231, 225-234 (2008)
doi: 10.1016/j.taap.2008.05.007
PMID 18589467
Predicting Intrinsic Aqueous Solubility by a Thermodynamic Cycle
D.S. Palmer, A. Llinàs, I. Morao, G.M. Day, J.M. Goodman, R.C. Glen & J.B.O. Mitchell
Molecular Pharmaceutics, 5, 266-279 (2008)
doi: 10.1021/mp7000878
PMID 18290628
Electronic Reprint Available here
Novel Hybrid Ultrafast Shape Descriptor Method for use in Virtual Screening
E.O. Cannon, F. Nigsch & J.B.O. Mitchell
Chemistry Central Journal 2:3 (2008)
doi: 10.1186/1752-153X-2-3
PMID 18282294
How to Winnow Actives from Inactives: Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow
F. Nigsch & J.B.O. Mitchell
Journal of Chemical Information and Modeling, 48, 306-318 (2008)
doi: 10.1021/ci700350n
PMID 18220378
Why Are Some Properties More Difficult To Predict than Others? A Study of QSPR Models of Solubility, Melting Point, and Log P
L.D. Hughes, D.S. Palmer, F. Nigsch & J.B.O. Mitchell
Journal of Chemical Information and Modeling, 48, 220-232 (2008)
doi: 10.1021/ci700307p
PMID 18186622
Electronic Reprint Available here
In Vitro Models For Processes Involved In Intestinal Absorption
F. Nigsch, W. Klaffke & S. Miret
Expert Opinion on Drug Metabolism and Toxicology, 3, 545-556 (2007)
doi: 10.1517/17425225.3.4.545
The Chemistry of Protein Catalysis
G.L. Holliday, D.E. Almonacid, J.B.O. Mitchell & J.M. Thornton
Journal of Molecular Biology, 372, 1261-1277 (2007)
doi: 10.1016/j.jmb.2007.07.034
PMID 17727879
The Geometry of Interactions Between Catalytic Residues and their Substrates
J.W. Torrance, G.L. Holliday, J.B.O. Mitchell & J.M. Thornton
Journal of Molecular Biology, 369, 1140-1152 (2007)
doi: 10.1016/j.jmb.2007.03.055
PMID 17466330
Using Reaction Mechanism to Measure Enzyme Similarity
N.M. O'Boyle, G.L. Holliday, D.E. Almonacid & J.B.O. Mitchell
Journal of Molecular Biology, 368, 1484-1499 (2007)
doi: 10.1016/j.jmb.2007.02.065
PMID 17400244
Support Vector Inductive Logic Programming Outperforms the Naive Bayes Classifier and Inductive Logic Programming for the Classification of Bioactive Chemical Compounds
E.O. Cannon, A. Amini, A. Bender, M.J.E. Sternberg, S.H. Muggleton, R.C. Glen & J.B.O. Mitchell
Journal of Computer-Aided Molecular Design, 21, 269-280 (2007)
doi: 10.1007/s10822-007-9113-3
PMID 17387437
A Semiempirical Approach to the Intra-Phycocyanin and Inter-Phycocyanin Fluorescence Resonance Energy-Transfer Pathways in Phycobilisomes.
Adelio R. Matamala, Daniel E. Almonacid, Maximiliano F. Figueroa, Jose Martinez-Oyanedel and Marta C. Bunster,
Journal of Computational Chemistry, 28, 1200-1207 (2007)
doi: 10.1002/jcc.20628
Scoring Functions and Enrichment: A Case Study on Hsp90
C. Konstantinou-Kirtay, J.B.O. Mitchell & J.A. Lumley,
BMC Bioinformatics, 8, 27 (2007)
doi: 10.1186/1471-2105-8-27
PMID 17257425
The structure at 2 A resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC-PC complex.
Carlos Contreras-Martel, Adelio Matamala, Carola Bruna, German Poo-Caamano, Daniel Almonacid, Maximiliano Figueroa, Jose Martínez-Oyanedel and Marta Bunster,
Biophysical Chemistry, 125, 388-396 (2007)
doi: 10.1016/j.bpc.2006.09.014
Random Forest Models to Predict Aqueous Solubility
D.S. Palmer, N.M. O'Boyle, R.C. Glen & J.B.O. Mitchell
Journal of Chemical Information and Modeling, 47, 150-158 (2007)
doi: 10.1021/ci060164k
PMID 17238260
Electronic Reprint Available here
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
G.L. Holliday, D.E. Almonacid, G.J. Bartlett, N.M. O'Boyle, J.W. Torrance, P. Murray-Rust, J.B.O. Mitchell
& J.M. Thornton,
Nucleic Acids Research, 35, D515-D520 (2007)
doi: 10.1093/nar/gkl774
PMID 17082206
Full text freely available: Open Access click here
Melting Point Prediction Employing k-nearest Neighbor Algorithms and Genetic Parameter Optimization
F. Nigsch, A. Bender, B. van Buuren, J. Tissen, E. Nigsch & J.B.O. Mitchell,
Journal of Chemical Information and Modeling, 46, 2412-2422 (2006)
doi: 10.1021/ci060149f
PMID 17125183
Electronic Reprint Available here
Chemoinformatics-based Classification of Prohibited Substances Employed for Doping in Sport
E.O. Cannon, A. Bender, D.S. Palmer & J.B.O. Mitchell,
Journal of Chemical Information and Modeling, 46, 2369-2380 (2006)
doi: 10.1021/ci0601160
PMID 17125180
Electronic Reprint Available here
Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint
E.O. Cannon & J.B.O. Mitchell,
Lecture Notes in Bioinformatics, 4216, 173-182 (2006)
doi: 10.1007/11875741
Electronic Preprint Available here
Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions
G.L. Holliday, P. Murray-Rust & H.S. Rzepa,
Journal of Chemical Information and Modeling, 46, 145-157 (2006)
doi: 10.1021/ci0502698
PMID 16426051
MACiE: a database of enzyme reaction mechanisms
G.L. Holliday, G.J. Bartlett, D.E. Almonacid, N.M. O'Boyle, P. Murray-Rust, J.M. Thornton & J.B.O. Mitchell,
Bioinformatics, 21, 4315-4316 (2005)
doi: 10.1093/bioinformatics/bti693
PMID 16188925
Full text freely available: Open Access click here
Communication and re-use of chemical information in bioscience
P. Murray-Rust, J.B.O. Mitchell & H.S. Rzepa,
BMC Bioinformatics, 6, 180 (2005)
doi: 10.1186/1471-2105-6-180
PMID 16026614
Chemistry in Bioinformatics
P. Murray-Rust, J.B.O. Mitchell & H.S. Rzepa,
BMC Bioinformatics, 6, 141 (2005)
doi: 10.1186/1471-2105-6-141
PMID 15941476
Knowledge Based Potentials: the Reverse Boltzmann Methodology, Virtual Screening and Molecular Weight Dependence
C. Konstantinou Kirtay, J.B.O. Mitchell & J.A. Lumley,
QSAR & Combinatorial Science, 24, 527-536 (2005)
doi: 10.1002/qsar.200430926
Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems
Chem. Soc. Rev., 8, 641 (2005)
Ground- and excited-state electronic structure of an emissive pyrazine-bridged ruthenium(II) dinuclear complex
J. Am. Chem. Soc., 127, 1229 (2005)
Ground vs. excited state interaction in ruthenium-thienyl dyads: implications for through bond interactions in multicomponent systems
J. Mol. Struct., 735-736, 123 (2005)
Kinetics of the polymer collapse transition: The role of hydrodynamics
N. Kikuchi, J. F. Ryder, C. M. Pooley and J. M. Yeomans
Physical Review E, 71, 061804 (2005)
Predicting protein-ligand binding affinities: a low scoring game?
P. M. Marsden, D. Puvanendrampillai, J.B.O. Mitchell & R. C. Glen,
Organic & Biomolecular Chemistry, 2, 3267-3273 (2004)
doi: 10.1039/B409570G
PMID 15534704
A structure-odour relationship study using EVA descriptors and hierarchical clustering
S. Takane & J.B.O. Mitchell,
Organic & Biomolecular Chemistry, 2, 3250-3255 (2004)
doi: 10.1039/B409802A
PMID 15534702
CMLSnap: Animated Reaction Mechanisms
G.L. Holliday, J.B.O. Mitchell & P. Murray-Rust,
Internet Journal of Chemistry, 7, 4 (2004)
Comparative evaluation of five scoring functions for accurate prediction of protein-ligand binding energy
D. Puvanendrampillai, P. M. Marsden, J.B.O. Mitchell & R. C. Glen,
Abstracts of Papers of the American Chemical Society 227: 224-COMP Part 1 MAR 28 2004
Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes
Dalton Trans., 3943 (2004)
Synthesis and characterisation of ruthenium complexes containing a pendent catechol ring
Dalton Trans., 514 (2004)
Classification and Computer Representation of Enzyme Reactions. Progress Towards the Development of MACiE.
G.L. Holliday, G.J. Bartlett, P. Murray-Rust, J.M. Thornton & J.B.O. Mitchell,
Abstracts of Papers of the American Chemical Society 226: 099-CINF Part 1 SEP 2003
Triazinone Tautomers: Solid Phase Energetics
J. Bailey, L.J. Kettle, J.C. Cherryman & J.B.O. Mitchell,
CrystEngComm, 5, 498-502 (2003)
doi: 10.1039/b313124f
Electronic Reprint Available by emailed request
Can we Predict Lattice Energy from Molecular Structure?
C. Ouvrard & J.B.O. Mitchell,
Acta Crystallographica B59, 676-685 (2003)
doi: 10.1107/S0108768103019025
PMID 14586090
Electronic Reprint Available here
Protein Ligand Database (PLD): Additional Understanding of the Nature and Specificity of Protein-Ligand Complexes
D. Puvanendrampillai & J.B.O. Mitchell,
Bioinformatics, 19, 1856-1857 (2003)
doi: 10.1093/bioinformatics/btg243
PMID 14512362
D-Amino Acid Residues in Peptides and Proteins,
J.B.O. Mitchell & J. Smith,
Proteins: Structure, Function & Genetics, 50, 563-571 (2003)
doi: 10.1002/prot.10320
PMID 12577262
Electronic Preprint Available here
Transport coefficients of a mesoscopic fluid dynamics model
N. Kikuchi, C. M. Pooley, J. F. Ryder and J. M. Yeomans
Journal of Chemical Physics, 119, 6388 (2003)
Sequence-Dependent DNA Structure: A Database of Octamer Structural Parameters
Eleanor J. Gardiner, Christopher A. Hunter, Martin J. Packer, David S. Palmer and Peter Willett
J. Mol. Biol. 332, 1025-1035 (2003)
Highly electron rich alkyl- and dialkyl- N-pyrrolidinyl phosphines: An evaluation of their electronic and structural properties
M L. Clarke, G. L. Holliday, A M. Z. Slawin, and J. D Woollins,
J. Chem. Soc., Dalton Trans., 6, 1093-1103, (2002)
The Relationship Between the Sequence Identities of Alpha Helical Proteins in the PDB and the Molecular Similarities of their Ligands,
J.B.O. Mitchell,
Journal of Chemical Information and Computer Sciences, 41, 1617-1622 (2001)
doi: 10.1021/ci010364q
PMID 11749588
Anisotropic Repulsion Potentials for Cyanuric Chloride (C3N3Cl3) and their Application to Modeling the Crystal Structures of Azaaromatic Chlorides,
J.B.O. Mitchell, S.L. Price, M. Leslie, D. Buttar & R.J. Roberts,
J. Phys. Chem. A., 105, 9961-9971 (2001)
doi: 10.1021/jp0125350
The
Determination of the Crystal Structure of Anhydrous Theophylline by
X-ray Powder Diffraction with a Systematic Search Algorithm, Lattice
Energy Calculations and 13C and 15N Solid-state
NMR: A Question of Polymorphism in a Given Unit Cell,
E.D.L. Smith, R.B. Hammond, K.J. Roberts, M.J. Jones, J.B.O. Mitchell,
S.L. Price, R.K. Harris, D.C. Apperley, J.C. Cherryman & R. Docherty,
J. Phys. Chem. B., 105, 5818-5826 (2001)
doi: 10.1021/jp002060x
Evaluation of a Knowledge-Based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes,
I. Nobeli, J.B.O. Mitchell, A. Alex & J.M. Thornton,
Journal of Computational Chemistry, 22, 673-688 (2001)
doi: 10.1002/jcc.1036
First examples of M-Se-P-N-N heterocycles
M L Clarke, G L Holliday, A M Z Slawin and J D Woollins
Inorg.Chem.Comm, 4, 115-118 (2001)
A
Systematic Non-empirical Method of Deriving Model Intermolecular Potentials
for Organic Molecules: Application to Amides,
J.B.O. Mitchell & S.L. Price,
J. Phys. Chem. A., 104, 10958-10971 (2000)
doi: 10.1021/jp002400e
Electrostatic Factors in DNA Intercalation,
C. Medhi, J.B.O. Mitchell, S.L. Price & A.B. Tabor,
Biopolymers (Nucleic Acid Science), 52, 84-93 (1999)
doi: 10.1002/1097-0282(1999)52:2<84::AID-BIP2>3.0.CO;2-S
PMID 10898854
BLEEP
- Potential of Mean Force Describing Protein-Ligand Interactions:
II. Calculation of Binding Energies and Comparison with Experimental
Data,
J.B.O. Mitchell, R.A. Laskowski, A. Alex, M.J. Forster & J.M.
Thornton,
Journal of Computational Chemistry, 20, 1177-1185 (1999)
doi: 10.1002/(SICI)1096-987X(199908)20:11<1177::AID-JCC8>3.0.CO;2-0
BLEEP
- Potential of Mean Force Describing Protein-Ligand Interactions:
I. Generating Potential,
J.B.O. Mitchell, R.A. Laskowski, A. Alex & J.M. Thornton,
Journal of Computational Chemistry, 20, 1165-1176 (1999)
doi: 10.1002/(SICI)1096-987X(199908)20:11<1165::AID-JCC7>3.0.CO;2-A
SATIS:
Atom Typing from Chemical Connectivity
J.B.O. Mitchell, A. Alex & M. Snarey,
Journal of Chemical Information and Computer Sciences, 39, 751-757 (1999)
doi: 10.1021/ci9904214
Protein Folds and Functions,
A.C.R. Martin, C.A. Orengo, E.G. Hutchinson, S. Jones, M. Karmirantzou,
R.A. Laskowski, J.B.O. Mitchell, C. Taroni & J.M. Thornton,
Structure, 6, 875-884 (1998)
doi: S0969-2126(98)00089-6
PMID 9687369
Design, Synthesis and Structure of a Zinc Finger with an Artificial beta-turn,
J.H. Viles, S.U. Patel, J.B.O. Mitchell, C.M. Moody, D.E. Justice, J. Uppenbrink, P.M. Doyle, C.J. Harris, P.J. Sadler & J.M. Thornton,
J. Mol. Biol., 279, 973-986 (1998)
doi: 10.1006/jmbi.1998.1764
PMID 9642075
Non-Randomness
in Side-Chain Packing: The Distribution of Interplanar Angles,
J.B.O. Mitchell, R.A. Laskowski & J.M. Thornton,
Proteins: Structure, Function & Genetics, 29, 370-380 (1997)
PMID 9365991
Multiple
Solution Conformations of the Integrin-Binding Cyclic Pentapeptide Cyclo-[Ser-D-Leu-Asp-Val-Pro]:
Analysis of the (phi,psi) Space Available to Cyclic Pentapeptides,
J.H. Viles, J.B.O. Mitchell, S.L. Gough, P.M. Doyle, C.J. Harris,
P.J. Sadler & J.M. Thornton,
Eur. J. Biochem., 242, 352-362 (1996)
doi: 10.1111/j.1432-1033.1996.0352r.x
PMID 8973654
Multipole-Based Calculation of the Polarization Energy,
J.B.O. Mitchell,
Theoretica Chimica Acta, 94, 287-295 (1996)
doi: 10.1007/BF00213713
Protein Recognition of Adenylate: An Example of a Fuzzy Recognition Template,
S.L. Moodie, J.B.O. Mitchell & J.M. Thornton,
J. Mol. Biol., 263, 486-500 (1996)
doi: 10.1006/jmbi.1996.0591
PMID 8918603
Modelling the
Interactions of Protein Side-chains,
J.B.O. Mitchell, J.M. Thornton & S.L. Price,
in `Modelling of Biomolecular Structures and Mechanisms' (eds. A. Pullman, J. Jortner & B. Pullman), (1995) pp. 119-135. (Proceedings of the 27th Jerusalem Symposium in Quantum Chemistry and Biochemistry, 1994)
Also published in Molecular Engineering, 5, 89-105 (1995)
Amino / Aromatic Interactions in Proteins: Is the Evidence Stacked Against Hydrogen Bonding?
J.B.O. Mitchell, C.L. Nandi, I.K. McDonald, J.M. Thornton &
S.L. Price,
J. Mol. Biol., 239, 315-331 (1994)
doi: 10.1006/jmbi.1994.1370
PMID 8196060
Gaussian Multipoles in Practice: Electrostatic Energies for Intermolecular Potentials,
R.J. Wheatley & J.B.O. Mitchell,
J. Comp. Chem., 15, 1187-1198 (1994)
doi: 10.1002/jcc.540151102
Amino-Aromatic
Interactions,
J.B.O. Mitchell, C.L. Nandi, S. Ali, I.K. McDonald, J.M. Thornton,
S.L. Price & J. Singh,
Nature, 366, 413 (1993)
doi: 10.1038/366413a0
Protein Structures
and Complexes: What they Reveal About the Interactions that Stabilize
them,
J.M. Thornton, M.W. MacArthur, I.K. McDonald, D.T. Jones, J.B.O.
Mitchell, C.L. Nandi, S.L. Price & M.J.J.M. Zvelebil,
Phil. Trans. R. Soc. Lond. A, 345, 113-129 (1993)
A Comparison of Three Theoretical Approaches to the Study of Side-chain Interactions in Proteins,
J.B.O. Mitchell, C.L. Nandi, J.M. Thornton, S.L. Price, J. Singh & M. Snarey,
J. Chem. Soc. Faraday Trans., 89, 2619-2630 (1993)
doi: 10.1039/FT9938902619
Towards an Understanding of the Arginine-Aspartate Interaction,
J.B.O. Mitchell, J.M. Thornton, J. Singh & S.L. Price,
J. Mol. Biol., 226, 251-262 (1992)
doi: 10.1016/0022-2836(92)90137-9
PMID 1619654
On the Relative Strengths of Amide...Amide and Amide...Water Hydrogen Bonds,
J.B.O. Mitchell & S.L. Price,
Chem. Phys. Lett., 180, 517-523 (1991)
doi: 10.1016/0009-2614(91)85003-F
The Nature of the N-H...O=C Hydrogen Bond: An Intermolecular Perturbation Theory Study of the Formamide / Formaldehyde Complex,
J.B.O. Mitchell & S.L. Price,
J. Comp. Chem., 11, 1217-1233 (1990)
doi: 10.1002/jcc.540111014
On the electrostatic directionality of N-H...O=C Hydrogen Bonding,
J.B.O. Mitchell & S.L. Price,
Chem. Phys. Lett., 154, 267-272 (1989)
doi: 10.1016/0009-2614(89)87461-5
Diisophorone and Related Compounds (Part 19),
F. Kurzer, J.B.O. Mitchell & J.N. Patel,
Monatsh. Chemie, 119, 195-213 (1988)