Group | John Mitchell | Peter Mann | Eugene Shrimpton-Phoenix | Alumni: Rachael Skyner | Ava Sih-Yu Chen | Rosanna Alderson | Daniel Almonacid | Pedro Ballester | Luna de Ferrari | Gemma Holliday | Robert Lowe | Richard Marchese Robinson | Lazaros Mavridis | James McDonagh | Hamse Mussa | Neetika Nath | Florian Nigsch | Noel O'Boyle | David Palmer

Revisiting the application of machine learning approaches in predicting aqueous solubility,
T Zheng, JBO Mitchell, S Dobson,
ACS Omega (2024),
doi: 10.1021/acsomega.4c06163

Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release,
BJ Read, JBO Mitchell, RG da Silva,
Communications Chemistry, 7, 77 (2024)
doi: 10.1038/s42004-024-01165-8

Crystal structure, steady-state and pre-steady-state kinetics of Acinetobacter baumannii ATP phosphoribosyltransferase,
BJ Read, AF Cadzow, MS Alphey, JBO Mitchell, RG da Silva,
Biochemistry, 63, 230-240 (2024)
doi: 10.1021/acs.biochem.3c00551

Robust identification of interactions between heat-stress responsive genes in the chicken brain using Bayesian networks and augmented expression data,
EA Videla Rodriguez, JBO Mitchell, VA Smith,
Scientific Reports. 14, 9019 (2024)
doi: 10.1038/s41598-024-58679-3

Computational Insights into the Catalytic Mechanism of Is-PETase: An Enzyme Capable of Degrading Poly(ethylene) Terephthalate,
E Shrimpton-Phoenix, JBO Mitchell, M Bühl
Physical Review E, 106, 014304 (2022)
doi: 10.1002/chem.202201728

Practical Application of a Bayesian Network Approach to Poultry Epigenetics and Stress,
EAV Rodriguez, F Pertille, C Guerrero-Bosagna, JBO Mitchell, P Jensen, VA Smith
BMC Bioinformatics, 23, 261 (2022)
doi: 10.1186/s12859-022-04800-0

N-strain epidemic model using bond percolation,
P Mann, VA Smith, JBO Mitchell, S Dobson
Physical Review E, 106, 014304 (2022)
doi: 10.1103/PhysRevE.106.014304

Degree correlations in graphs with clique clustering,
P Mann, VA Smith, JBO Mitchell, S Dobson
Physical Review E, 105, 044314 (2022)
doi: 10.1103/PhysRevE.105.044314

Allosteric inhibition of Acinetobacter baumannii ATP phosphoribosyltransferase by protein:dipeptide and protein:protein interactions,
BJ Read, G Fisher, OLR Wissett, TFG Machado, J Nicholson, JBO Mitchell, RG da Silva,
ACS Infectious Diseases. 8: 197-209 (2022)
doi: 10.1021/acsinfecdis.1c00539

EAV Rodriguez, JBO Mitchell, VA Smith,
A Bayesian Network Structure Learning Approach to Identify Genes Associated with Stress in Spleens of Chickens,
Scientific Reports 12, 7482 (2022)
doi: 10.1038/s41598-022-11633-7

Toward physics-based solubility computation for pharmaceuticals to rival informatics,
DJ Fowles, DS Palmer, R Guo, SL Price, JBO Mitchell,
J. Chem. Theor. Comput., 17, 3700-3709 (2021)
doi: 10.1021/acs.jctc.1c00130

Exact formula for bond percolation on cliques,
P Mann, VA Smith, JBO Mitchell, CA Jefferson, S Dobson
Physical Review E, 104, 024304 (2021)
doi: 10.1103/PhysRevE.104.024304

Symbiotic and antagonistic disease dynamics on clustered networks using bond percolation,
P Mann, VA Smith, JBO Mitchell, S Dobson
Physical Review E, 104, 024303 (2021)
doi: 10.1103/PhysRevE.104.024303

Two-pathogen model with competition on clustered networks,
P Mann, VA Smith, JBO Mitchell, S Dobson,
Physical Review E, 103, 062308 (2021)
doi: 10.1103/PhysRevE.103.062308

Cooperative coinfection dynamics on clustered networks,
P Mann, VA Smith, JBO Mitchell, S Dobson,
Physical Review E, 103, 042307 (2021)
doi: 10.1103/PhysRevE.103.042307

Percolation in random graphs with higher-order clustering,
P Mann, VA Smith, JBO Mitchell, S Dobson,
Physical Review E, 103, 012313 (2021)
doi: 10.1103/PhysRevE.103.012313

Random graphs with arbitrary clustering and their applications,
P Mann, VA Smith, JBO Mitchell, S Dobson,
Physical Review E, 103, 012309 (2021)
doi: 10.1103/PhysRevE.103.012309

Three machine learning models for the 2019 Solubility Challenge,
J. B. O. Mitchell,
ADMET & DMPK 8, 215-251 (2020)
doi: 10.5599/admet.835

In silico methods to predict solubility,
J. L. McDonagh, J. B. O. Mitchell, D. S. Palmer & R. E. Skyner,
in Solubility in Pharmaceutical Chemistry (Eds C Saal & A Nair), De Gruyter (2020)
ISBN 978-3-11-055983-5

We are probably not Sims
J. B. O. Mitchell
Science & Christian Belief, 32, 45-62 (2020)

Rational drug design of antineoplastic agents using 3D-QSAR, cheminformatic, and virtual screening approaches
J. Vucicevic, K. Nikolic & J.B.O. Mitchell
Current Medicinal Chemistry, 26, 3874-3889 (2019)
doi: 10.2174/0929867324666170712115411
PMID: 28707592

Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion
M. Addicoat, C. S. Adjiman, M. Arhangelskis, G. J. O. Beran, D. Bowskill, J. G. Brandenburg, D. E. Braun, V. Burger, J. Cole, A. J. Cruz-Cabeza, G. M. Day, V. L. Deringer, R. Guo, A. Hare, J. Helfferich, J. Hoja, L. Iuzzolino, S. Jobbins, N. Marom, D. McKay, J. B. O. Mitchell, S. Mohamed, M. Neumann, S. Nilsson Lill, J. Nyman, A. R. Oganov, P. Piaggi, S. L. Price, S. Reutzel-Edens, I. Rietveld, M. Ruggiero, M. R. Ryder, G. Sastre, J. C. Schön, C. Taylor, A. Tkatchenko, S. Tsuzuki, J. van den Ende, S. M. Woodley, G. Woollam & Q. Zhu
Faraday Discuss, 211, 325-381 (2018)
doi: 10.1039/C8FD90031K
PMID: 30302459

Applications of crystal structure prediction – organic molecular structures: general discussion
C. S. Adjiman, J. G. Brandenburg, D. E. Braun, J. Cole, C. Collins, A. I. Cooper, A. J. Cruz-Cabeza, G. M. Day, M. Dudek, A. Hare, L. Iuzzolino, D. McKay, J. B. O. Mitchell, S. Mohamed, S. Neelamraju, M. Neumann, S. Nilsson Lill, J. Nyman, A. R. Oganov, S. L. Price, A. Pulido, S. Reutzel-Edens, I. Rietveld, M. T. Ruggiero, J. C. Schön, S. Tsuzuki, J. van den Ende, G. Woollam & Q. Zhu
Faraday Discuss, 211, 493-539 (2018)
doi: 10.1039/C8FD90032A
PMID: 30285020

Applications of crystal structure prediction – inorganic and network structures: general discussion
V. Burger, F. Claeyssens, D. W. Davies, G. M. Day, M. S. Dyer, A. Hare, Y. Li, C. Mellot-Draznieks, J. B. O. Mitchell, S. Mohamed, A. R. Oganov, S. L. Price, M. Ruggiero, M. R. Ryder, G. Sastre, J. C. Schön, P. Spackman, S. M. Woodley & Q. Zhu
Faraday Discuss, 211, 613-642 (2018)
doi: 10.1039/C8FD90034E
PMID: 30298165

Artificial Intelligence in Pharmaceutical Research and Development
J.B.O. Mitchell
Future Medicinal Chemistry, 10, 1529-1531 (2018)
doi: 10.4155/fmc-2018-0158
PMID: 29966438

Can human experts predict solubility better than computers?
S. Boobier, A. Osbourn & J.B.O. Mitchell
Journal of Cheminformatics, 9:63 (2017)
doi: 10.1186/s13321-017-0250-y
PMID: 29238891
   

Enzyme function and its evolution
J.B.O. Mitchell
Current Opinion in Structural Biology, 47, 151-156 (2017)
doi: 10.1016/j.sbi.2017.10.004
PMID: 29107208

Probing the average distribution of water in organic hydrate crystal structures with radial distribution functions (RDFs)
R.E. Skyner, J.B.O. Mitchell & C.R. Groom
CrystEngComm, 19, 641-652 (2017)
doi: 10.1039/C6CE02119K

Are the sublimation thermodynamics of organic molecules predictable?
J.L. McDonagh, D.S. Palmer, T. van Mourik & J.B.O. Mitchell
J. Chem. Inf. Model., 56, 2162-2179 (2016)
doi: 10.1021/acs.jcim.6b00033

Drug design for CNS diseases: polypharmacological profiling of compounds using cheminformatic, 3D-QSAR and virtual screening methodologies
K. Nikolic, L. Mavridis, T. Djikic, J. Vucicevic, D. Agbaba, K. Yelekci & J.B.O. Mitchell
Frontiers in Neuroscience, 10:265, 18-38 (2016)
doi: 10.3389/fnins.2016.00265

A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins
A.S.-Y. Chen, N.J. Westwood, P. Brear, G.W. Rogers, L. Mavridis & J.B.O. Mitchell
Molecular Informatics, 35, 125-135 (2016)
doi: 10.1002/minf.201500108

A note on utilising binary features as ligand descriptors
H.Y. Mussa, J.B.O. Mitchell & R.C. Glen
Journal of Cheminformatics, 7:58 (2015)
doi: 10.1186/s13321-015-0105-3
PMID: 26628925
   

Enzyme Mechanism Prediction: A Template Matching Problem on InterPro Signature Subspaces
H.Y. Mussa, L. De Ferrari & J.B.O. Mitchell
BMC Research Reports, 8:744 (2015)
doi: 10.1186/s13104-015-1730-7
PMID: 26634450
   

Why do sequence signatures predict enzyme mechanism? Homology versus Chemistry
K.E. Beattie, L. De Ferrari & J.B.O. Mitchell
Evolutionary Bioinformatics, 11, 267-274 (2015)
doi: 10.4137/EBO.S31482
PMID: 26740739
   

Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation
J.L. McDonagh, T. van Mourik & J.B.O. Mitchell
Molecular Informatics, 34, 715-724 (2015)
doi: 10.1002/minf.201500052

The Parzen Window method: In terms of two vectors and one matrix
H.Y. Mussa, J.B.O. Mitchell & A.M. Afzal
Pattern Recognition Letters, 63, 30-35 (2015)
doi: 10.1016/j.patrec.2015.06.002
PMID: 26435560

Verifying the fully "Laplacianised" posterior Naive Bayesian approach and more
H.Y. Mussa, D. Marcus, J.B.O. Mitchell & R.C. Glen
Journal of Cheminformatics, 7:27 (2015)
doi: 10.1186/s13321-015-0075-5
PMID: 26075027
   

Greedy and Linear Ensembles of Machine Learning Methods Outperform Single Approaches for QSPR Regression Problems
W. Kew & J.B.O. Mitchell
Molecular Informatics 34, 634-647 (2015)
doi: 10.1002/minf.201400122

A Review of Methods for the Calculation of Solution Free Energies and the Modelling of Systems in Solution
R.E. Skyner, J.L. McDonagh, C.R. Groom, T. van Mourik & J.B.O. Mitchell
Physical Chemistry Chemical Physics, 17, 6174-6191 (2015)
doi: 10.1039/C5CP00288E
PMID: 25660403
   

Predicting targets of compounds against neurological diseases using cheminformatic methodology
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
Journal of Computer-Aided Molecular Design, 29, 183-188 (2015)
doi: 10.1007/s10822-014-9816-1
PMID: 25425329

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
R.G. Alderson, D. Barker & J.B.O. Mitchell
Journal of Molecular Evolution, 79, 117-129 (2014)
doi: 10.1007/s00239-014-9639-7
PMID: 25185655
   

Is Experimental Data Quality the Limiting Factor in Predicting the Aqueous Solubility of Druglike Molecules?
D.S. Palmer & J.B.O. Mitchell
Molecular Pharmaceutics, 11, 2962-2972 (2014)
doi: 10.1021/mp500103r
PMID: 24919008
  

The Natural History of Biocatalytic Mechanisms
N. Nath, J.B.O. Mitchell & G. Caetano-Anollés
PLoS Computational Biology, 10, e1003642 (2014)
doi: 10.1371/journal.pcbi.1003642
PMID: 24874434
   

From sequence to enzyme mechanism using multi-label machine learning
L. De Ferrari & J.B.O. Mitchell
BMC Bioinformatics, 15:150 (2014)
doi: 10.1186/1471-2105-15-150
PMID: 24885296
   

Uniting Cheminformatics and Chemical Theory to Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules
J.L. McDonagh, N. Nath, L. De Ferrari, T. van Mourik & J.B.O. Mitchell
J. Chem. Inf. Model., 54, 844-856 (2014)
doi: 10.1021/ci4005805
PMID: 24564264
   

Machine learning methods in chemoinformatics
J.B.O. Mitchell
WIREs Comput. Mol. Sci., 4, 468-481 (2014)
doi: 10.1002/wcms.1183
PMID: 25285160
   

PFClust: an optimised implementation of a parameter-free clustering algorithm
K. Musayeva, T. Henderson, J.B.O. Mitchell & L. Mavridis
Source Code for Biology and Medicine, 9:5 (2014)
doi: 10.1186/1751-0473-9-5
PMID: 24490618
   

Full "Laplacianised" posterior naive Bayesian algorithm
H.Y. Mussa, J.B.O. Mitchell & R.C. Glen
Journal of Cheminformatics, 5:37 (2013)
doi: 10.1186/1758-2946-5-37
PMID: 23968281
   

4273pi: Bioinformatics education on low cost ARM hardware
D. Barker, D.E.K. Ferrier, P.W.H. Holland, J.B.O. Mitchell, H. Plaisier, M.G. Ritchie & S.D. Smart
BMC Bioinformatics, 14:243 (2013)
doi: 10.1186/1471-2105-14-243
PMID: 23937194
   

In silico target predictions: defining a benchmarking dataset and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt Window
A. Koutsoukas, R. Lowe, Y. KalantarMotamedi, H. Y. Mussa, W. Klaffke, J. B. O. Mitchell, R. C. Glen & A. Bender
J. Chem. Inf. Model. 53, 1957-1966 (2013)
doi: 10.1021/ci300435j
PMID 23829430

PFClust: a novel parameter free clustering algorithm
L. Mavridis, N. Nath & J.B.O. Mitchell
BMC Bioinformatics, 14:213 (2013)
doi: 10.1186/1471-2105-14-213
PMID 23819480
   

Predicting the protein targets for athletic performance-enhancing substances
L. Mavridis & J.B.O. Mitchell
Journal of Cheminformatics, 5:31 (2013)
doi: 10.1186/1758-2946-5-31
PMID 23800040
   

Enzyme Informatics
R.G. Alderson, L. De Ferrari, L. Mavridis, J.L. McDonagh, J.B.O. Mitchell & N. Nath
Current Topics in Medicinal Chemistry, 12, 1911-1923 (2012)
doi: 10.2174/1568026611209061911
PMID 23116471

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
P.J. Ballester, M. Mangold, N.I. Howard, R.L. Marchese Robinson, C. Abell, J. Blumberger & J.B.O. Mitchell
J. R. Soc. Interface, 9, 3196-3207 (2012)
doi: 10.1098/rsif.2012.0569
PMID 22933186
   

First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules
D.S. Palmer, J.L. McDonagh, J.B.O. Mitchell, T. van Mourik & M.V. Fedorov
J. Chem. Theory Comput., 8, 3322-3337 (2012)
doi: 10.1021/ct300345m

Is EC class predictable from reaction mechanism?
N. Nath & J.B.O. Mitchell
BMC Bioinformatics, 13:60 (2012)
doi: 10.1186/1471-2105-13-60
PMID 22530800
   

Predicting the mechanism of phospholipidosis
R. Lowe, H.Y. Mussa, F. Nigsch, R.C. Glen & J.B.O. Mitchell
Journal of Cheminformatics, 4:2 (2012)
doi: 10.1186/1758-2946-4-2
PMID 22281160
   

Classifying Molecules Using a Sparse Probabilistic Kernel Binary Classifier
R. Lowe, H.Y. Mussa, J.B.O. Mitchell & R.C. Glen
Journal of Chemical Information and Modeling, 51, 1539-1544 (2011)
doi: 10.1021/ci200128w
PMID 21696153

Characterising the complexity of enzymes based on their mechanisms and structures using a bio-computational analysis
G.L. Holliday, J.D. Fischer, J.B.O. Mitchell & J.M. Thornton
FEBS Journal, 278, 3835-3845 (2011)
doi: 10.1111/j.1742-4658.2011.08190.x
PMID 21605342

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
P.J. Ballester & J.B.O. Mitchell
Journal of Chemical Information and Modeling, 51, 1739-1741 (2011)
doi: 10.1021/ci200057e
PMID 21591735

Development and Comparison of hERG Blocker Classifiers: Assessment on Different Datasets Yields Markedly Different Results
R. L. Marchese Robinson, R.C. Glen & J.B.O. Mitchell
Molecular Informatics, 30, 443-458 (2011)
doi: 10.1002/minf.201000159

Informatics, machine learning and computational medicinal chemistry
J.B.O. Mitchell
Future Medicinal Chemistry, 3, 451-467 (2011)
doi: 10.4155/fmc.11.11
PMID 21452981

Ask the experts: focus on computational chemistry
J. Bajorath, M. L. Barreca, A. Bender, R. Bryce, M. Hutter, C. Laggner, C. Laughton, Y. Martin, J. B. O. Mitchell, A. Padova, S. Renner, P. M. Selzer, W. Sherman, W. Sippl, C. Taft, T. Tuccinardi, G. Vistoli & P. Willett
Future Medicinal Chemistry, 3, 909-921 (2011)
doi: 10.4155/fmc.11.57
PMID 21707395

Predicting Phospholipidosis using Machine Learning
R. Lowe, R.C. Glen & J.B.O. Mitchell
Molecular Pharmaceutics, 7, 1708-1714 (2010)
doi: 10.1021/mp100103e
PMID 20799726
   

A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
P.J. Ballester & J.B.O. Mitchell
Bioinformatics, 26, 1169-1175 (2010)
doi: 10.1093/bioinformatics/btq112
PMID 20236947

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, 6:e1000700 (2010)
doi: 10.1371/journal.pcbi.1000700
PMID 20300652
   

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

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

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

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

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

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

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

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

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: 10.1016/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)
doi: 10.1007/BF00999581

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)
doi: 10.1098/rsta.1993.0123

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)
doi: 10.1007/BF00809594