2013

The EBI enzyme portal
Alcántara, R., ONWUBIKO J., CAO H., De Matos P., Cham J. A., JACOBSEN J., HOLLIDAY G. L., FISCHER J. D., RAHMAN S. A., Jassal B., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D773–D780

2012

Open data for drug discovery: learning from the biological community
HERSEY, A., Senger S., and OVERINGTON J. P.
Future medicinal chemistry. Oct, Volume 4, Number 15, (2012), p.1865-1867
Global analysis of small molecule binding to related protein targets
KRUGER, F. A., and OVERINGTON J. P.
PLoS computational biology. Jan, Volume 8, Number 1, (2012), p.e1002333
Annotating human P-glycoprotein bioassay data
Zdrazil, B., Pinto M., Vasanthanathan P., Williams A. J., Balderud L. Z., Engkvist O., Chichester C., HERSEY A., OVERINGTON J. P., and Ecker G. F.
Molecular Informatics. Volume 31, Number 8, (2012), p.599-609
Annotating Human P-Glycoprotein Bioassay Data
Zdrazil, B., Pinto M., Vasanthanathan P., Williams A. J., Balderud L. Z., Engkvist O., Chichester C., HERSEY A., OVERINGTON J. P., and Ecker G. F.
Molecular Informatics. Volume 31, Number 8, (2012), p.599–609
Cheminformatics
Wegner, J. K., Sterling A., Guha R., Bender A., Faulon, HASTINGS J., O'Boyle N., OVERINGTON J., Vlijmen Van H., and Willighagen E.
Commun.ACM. nov, Volume 55, Number 11, (2012), p.65-75
Shouldn't enantiomeric purity be included in the'minimum information about a bioactive entity? Response from the MIABE group
Orchard, S., Al-Lazikani B., Bryant S., Clark D., Calder E., DIX I., Engkvist O., Forster M., GAULTON A., Gilson M., et al.
Nature Reviews Drug Discovery. Volume 11, Number 9, (2012), p.730–730 doi:
Toxicogenomics Investigation Under the eTOX Project
Taboureau, O., HERSEY A., Audouze K., Gautier L., Jacobsen UP, Akhtar R., F A., and Brunak S O. J. P.
J Pharmacogenom Pharmacoproteomics. Volume 7, (2012), p.2153–0645
Open data for drug discovery: learning from the biological community
HERSEY, A., Senger S., and OVERINGTON J. P.
Future Med. Chem.. Volume 4, Number 15, (2012), p.1865–1867
Chemogenomics, Introduction to Cheminformatics: Data management, manipulation and properties,
OVERINGTON, J. P.
(2012),
Cheminformatics
Wegner, J. K., Sterling A., Guha R., Bender A., Faulon J. L., HASTINGS J., O'Boyle N., OVERINGTON J., Van Vlijmen H., and Willighagen E.
Communications of the ACM. Volume 55, Number 11, (2012), p.65–75
Mapping small molecule binding data to structural domains
KRUGER, F. A., Rostom R., and OVERINGTON J. P.
BMC Bioinformatics. Volume 13, Number Suppl 17, (2012), p.S11
Global Analysis of Small Molecule Binding to Related Protein Targets
KRUGER, F. A., and OVERINGTON J. P.
PLoS Computational Biology. Volume 8, Number 1, (2012), p.e1002333
ChEMBL: a large-scale bioactivity database for drug discovery
GAULTON, A., BELLIS L. J., BENTO A. P., CHAMBERS J., DAVIES M., HERSEY A., LIGHT Y., MCGLINCHEY S., Michalovich D., Al-Lazikani B., et al.
Nucleic acids research. Sep 23, Volume 40, Number Database issue, (2012), p.D1100-D1107

2011

Collation and data-mining of literature bioactivity data for drug discovery
BELLIS, L. J., Akhtar R., AlLazikani B., ATKINSON F., BENTO A. P., CHAMBERS J., DAVIES M., GAULTON A., HERSEY A., IKEDA K., et al.
Biochemical Society Transactions. Volume 39, Number 5, (2011), p.1365
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
ARANDA, B., Blankenburg H., KERRIEN S., Brinkman F. S. L., Ceol A., Chautard E., DANA J. M., De Las Rivas J., DUMOUSSEAU M., Galeota E., et al.
Nature methods. Volume 8, Number 7, (2011), p.528–529
ChEMBL: a large-scale bioactivity database for drug discovery
GAULTON, A., BELLIS L. J., BENTO A. P., CHAMBERS J., DAVIES M., HERSEY A., LIGHT Y., MCGLINCHEY S., Michalovich D., Al-Lazikani B., et al.
Nucleic Acids Research. (2011),
Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space
van der Horst, E., E Peironcely J., JP van Westen G., O van den Hoven O., RJD Galloway W., R Spring D., Wegner J. K., WT van Vlijmen H., P IJzerman A., OVERINGTON J. P., et al.
Current Topics in Medicinal Chemistry. Volume 11, Number 15, (2011), p.1964–1977
Rapid Analysis of Pharmacology for Infectious Diseases
Hopkins, A. L., Richard Bickerton G., Carruthers I. M., K Boyer S., Rubin H., and OVERINGTON J. P.
Current Topics in Medicinal Chemistry. Volume 11, Number 10, (2011), p.1292–1300
Minimum information about a bioactive entity (MIABE)
Orchard, S., Al-Lazikani B., Bryant S., Clark D., Calder E., DIX I., Engkvist O., Forster M., GAULTON A., Gilson M., et al.
Nature Reviews Drug Discovery. Volume 10, Number 9, (2011), p.661–669 doi:
Probing the links between in vitro potency, ADMET and physicochemical parameters
Gleeson, M. P., HERSEY A., Montanari D., and OVERINGTON J.
Nature Reviews Drug Discovery. Volume 10, Number 3, (2011), p.197–208

2010

Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens
Magariños, M. P., OVERINGTON J., Carmona S., Shanmugam D., Doyle M., Ralph S., Crowther G., Hertz-Fowler C., Nwaka S., Berriman M., et al.
BMC Bioinformatics. Volume 11, Number Suppl 10, (2010), p.O10
Role of open chemical data in aiding drug discovery and design
GAULTON, A., and OVERINGTON J. P.
Future Med Chem. Volume 2, Number 6, (2010), p.903–907
Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation
ABAD-ZAPATERO, C., Perisic O., Wass J., BENTO A. P., OVERINGTON J., Al-Lazikani B., and Johnson M. E.
Drug discovery today. Volume 15, Number 19-20, (2010), p.804–811

2009

New open drug activity data at EBI
Steinbeck, C., Al-Lazikani B., Hermjakob H., OVERINGTON J., and Thornton J.
Chemistry Central Journal. Volume 3, (2009), p.1–1
The genome of the blood fluke Schistosoma mansoni
Berriman, M., Haas B. J., LoVerde P. T., Wilson R. A., Dillon G. P., Cerqueira G. C., Mashiyama S. T., Al-Lazikani B., Andrade L. F., Ashton P. D., et al.
Nature. Volume 460, Number 7253, (2009), p.352–358
ChEMBL. an interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute outstation of the European Molecular Biology Laboratory (EMBL-EBI)
OVERINGTON, J.
Journal of computer-aided molecular design. Volume 23, Number 4, (2009), p.195–198

2008

MODELLER. A Program for Protein Structure Modeling
Šali, A., Webb B., Madhusudhan MS, Shen MY, Marti-Renom MA, Eswar N., Alber F., Topf M., Oliva B., Fiser A., et al.
(2008),
Genomic-scale prioritization of drug targets: the TDR Targets database
Agüero, F., Al-Lazikani B., Aslett M., Berriman M., Buckner F. S., Campbell R. K., Carmona S., Carruthers I. M., Chan A. W. E., Chen F., et al.
Nature Reviews Drug Discovery. Volume 7, Number 11, (2008), p.900–907
The molecular basis of predicting druggability
Al-Lazikani, B., GAULTON A., Paolini G., Lanfear J., OVERINGTON J., and Hopkins A.
(2008),

2007

Knowledge-based prediction for alternate indications and targets for known drugs
Chan, A. W. E., and OVERINGTON J.
234th National ACS Meeting, Boston. (2007),

2006

In silico compound activity reprofiling
Chan, A. W. E., Fagan RJ, and OVERINGTON J. P.
(2006),
How many drug targets are there?
OVERINGTON, J. P., Al-Lazikani B., and Hopkins A. L.
Nature Reviews Drug discovery. Volume 5, Number 12, (2006), p.993–996
Can we rationally design promiscuous drugs?
Hopkins, A. L., Mason J. S., and OVERINGTON J. P.
Current opinion in structural biology. Volume 16, Number 1, (2006), p.127–136

2005

Chemogenomic assessment of SAR data from learned journals
Cox, R., Chan A. W. E., Al-Lazikani B., Michalovich D., and OVERINGTON J. P.
230th National ACS Meeting, Washington DC. Volume 230, (2005), p.U1035–U1035
Modulating Cell Activity By Using An Agent That Reduces The Level Of Cholesterol Within a Cell
Allen, J., and OVERINGTON J. P.
(2005),
GPCR Knowledge Base - From Sequences to Ligands.
Chan, A. W. E., Al-Lazikani B., Carruthers I., Cox R., Dann S., DAVIES M., Michalovich D., and OVERINGTON J.
229th National ACS Meeting, San Diego. Volume 229, (2005),

2004

PDBLIG: classification of small molecular protein binding in the Protein Data Bank
Chalk, A. J., Worth C. L., OVERINGTON J. P., and Chan A. W. E.
Journal of medicinal chemistry. Volume 47, Number 15, (2004), p.3807–3816
Pleiotropic effects of Statins
Floto, A., OVERINGTON J., and Allen J.
Annual Reports in Medicinal Chemistry. Volume 39, (2004), p.239–258

2003

Consensus pharmacophore models for gene family analyses
Brandl, M. B., OVERINGTON J. P., and Chan A. W. E.
New Approaches in Drug Design and Discovery, University of Marburg. (2003),
Recent development in cheminformatics and chemogenomics
Edith Chan, AW, and OVERINGTON J. P.
Annual Reports in Medicinal Chemistry. Volume 38, (2003), p.285–294

2002

Expanding and exploring cellular pathways for novel drug targets
Weir, M. P., OVERINGTON J. P., and Schwarz M.
Annual Reports in Medicinal Chemistry. Volume 37, (2002), p.187–196
Protein sequence analysis in silico: application of structure-based bioinformatics to genomic initiatives
Michalovich, D., OVERINGTON J., and Fagan R.
Current opinion in pharmacology. Volume 2, Number 5, (2002), p.574–580
Design of selective thrombin inhibitors based on the (R)-Phe-Pro-Arg sequence
Danilewicz, J. C., Abel S. M., Brown A. D., Paul V., Hawkeswood E., Holland S. J., James K., McElroy A. B., OVERINGTON J., Michael J., et al.
Journal of medicinal chemistry. Volume 45, Number 12, (2002), p.2432–2453
Prioritizing the proteome: identifying pharmaceutically relevant targets
Swindells, M. B., and OVERINGTON J. P.
Drug Discovery Today. Volume 7, Number 9, (2002), p.516–521
Nicastrin Protein
Fagan, RJ, OVERINGTON J. P., Swindells M. B., and Weir M.
(2002),
Synthesis of macrocyclic, potential protease inhibitors using a generic scaffold
Dumez, E., Snaith J. S., Jackson R. F. W., McElroy A. B., OVERINGTON J., Wythes M. J., Withka J. M., and McLellan T. J.
The Journal of Organic Chemistry. Volume 67, Number 14, (2002), p.4882–4892

2001

Insights into protein function through large-scale computational analysis of sequence and structure
Weir, M., Swindells M., and OVERINGTON J.
Trends in Biotechnology. Volume 19, (2001), p.61–66
Nicastrin, a presenilin-interacting protein, contains an aminopeptidase/transferrin receptor superfamily domain
Fagan, R., Swindells M., OVERINGTON J., and Weir M.
Trends in biochemical sciences. Volume 26, Number 4, (2001), p.213–214

1998

Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies
Sowdhamini, R., Burke D. F., Deane C., Huang J., Mizuguchi K., Nagarajaram H. A., OVERINGTON J. P., Srinivasan N., Steward RE, and Blundell T. L.
Acta Crystallographica Section D: Biological Crystallography. Volume 54, Number 6, (1998), p.1168–1177
JOY: protein sequence-structure representation and analysis.
Mizuguchi, K., Deane C. M., Blundell T. L., Johnson M. S., and OVERINGTON J. P.
Bioinformatics. Volume 14, Number 7, (1998), p.617–623
The Discovery of UK-156,406 An orally active thrombin inhibitor
Allen, M., Abel S. M., Barber CG, Cussans NJ, Danilewicz J. C., Ellis D., Hawkeswood E., Herron M., Holland S., Fox DNA, et al.
Book of Abstracts, 215th ACS National Meeting, Dallas. (1998),
HOMSTRAD: a database of protein structure alignments for homologous families
Mizuguchi, K., Deane C. M., Blundell T. L., and OVERINGTON J. P.
Protein Science. Volume 7, Number 11, (1998), p.2469–2471

1996

Discrimination of common protein folds: Application of protein structure to sequence/structure comparisons
Johnson, M. S., May A. C. W., Rodionov M. A., and OVERINGTON J. P.
Methods in enzymology. Volume 266, (1996), p.575–598

1995

Probing Bacteriocin 28B Membrane Insertion by Disulphide Bond Engineering
Enfedaque, J., OVERINGTON J., Pattus F., and Regue M.
Protein Engineering. Volume 8, (1995), p.45

1994

Derivation of rules for comparative protein modeling from a database of protein structure alignments
Šali, A., and OVERINGTON J. P.
Protein Science. Volume 3, Number 9, (1994), p.1582–1596
The prediction and orientation of $\alpha$-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules
Donnelly, D., OVERINGTON J. P., and Blundell T. L.
Protein engineering. Volume 7, Number 5, (1994), p.645
Comparative modelling of major house dust mite allergen Der pI: Structure validation using an extended environmental amino acid propensity table
Topham, C. M., Srinivasan N., Thorpe C. J., OVERINGTON J. P., and Kalsheker N. A.
Protein engineering. Volume 7, Number 7, (1994), p.869
The comparison of structures and sequences: alignment, searching and the detection of common folds
Johnson, M. S., OVERINGTON J. P., Edwards Y., May A. C. W., and Rodionov M. A.
System Sciences, 1994. Vol. V: Biotechnology Computing, Proceedings of the Twenty-Seventh Hawaii International Conference on. Volume 5, (1994), p.296–305

1993

Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure
Hoffrén, A. M., Saloheimo M., Thomas P., OVERINGTON J. P., Johnson M. S., Knowles J. K. C., and Blundell T. L.
Protein engineering. Volume 6, Number 2, (1993), p.177
A Structural Basis for Sequence Comparisons:: An Evaluation of Scoring Methodologies
Johnson, M. S., and OVERINGTON J. P.
Journal of molecular biology. Volume 233, Number 4, (1993), p.716–738
Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins
OVERINGTON, J. P., HU Z. Z., Šali A., Johnson M. S., Sowdhamini R., Louie GV, and Blundell T. L.
Biochemical Society transactions. Volume 21, (1993), p.597–604
Modeling $\alpha$-helical transmembrane domains: The calculation and use of substitution tables for lipid-facing residues
Blundell, T. L., Donnelly D., OVERINGTON J. P., Ruffle S. V., and Nugent J. H. A.
Protein Science. Volume 2, Number 1, (1993), p.55–70
Alignment and searching for common protein folds using a data bank of structural templates
Johnson, M. S., OVERINGTON J. P., and Blundell T. L.
Journal of molecular biology. Volume 231, Number 3, (1993), p.735–752
Fragment Ranking in Modelling of Protein Structure:: Conformationally Constrained Environmental Amino Acid Substitution Tables
Topham, C. M., McLeod A., Eisenmenger F., OVERINGTON J. P., Johnson M. S., and Blundell T. L.
J. Mol. Biol. Volume 229, (1993), p.194–220

1992

Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
OVERINGTON, J., Donnelly D., Johnson M. S., Šali A., and Blundell T. L.
Protein Science. Volume 1, Number 2, (1992), p.216–226
Structural constraints on residue substitution.
OVERINGTON, J.
Genetic engineering. Volume 14, (1992), p.231
Comparison of three-dimensional structures of homologous proteins
OVERINGTON, J. P.
Current Opinion in Structural Biology. Volume 2, Number 3, (1992), p.394–401
From Modelling Homologous Proteins To Prediction Of Structure
Šali, A., OVERINGTON J. P., Johnson M. S., and Blundell T. L.
(1992),

1991

Patterns of sequence variation in families of homologous proteins
Blundell, T. L., Cooper J., Donnelly D., Driessen H., Edwards Y., Eisenmenger F., Frazao C., Johnson M., Niefind K., Newman M., et al.
Methods in Protein Sequence Analysis. Birkhauser Verlag AG, Basel. (1991), p.373–385
Structure-function relationships in the cysteine proteinases actinidin, papain and papaya proteinase omega.
Topham, C. M., Salih E., Frazao C., Kowlessur D., OVERINGTON J. P., Thomas M., Brocklehurst SM, Patel M., Thomas EW, and Brocklehurst K.
Biochemical Journal. Volume 280, Number Pt 1, (1991), p.79
Knowledge-base Protein Modelling
OVERINGTON, J. P.
(1991),
Modelling the lignin peroxidase LIII of Phlebia radiata using a knowledge-based approach
Hoffrén, A. M., Saloheimo M., Thomas P., OVERINGTON J., Johnson M., and Blundell TT
AIP Conference Proceedings. Volume 239, (1991), p.346

1990

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction
OVERINGTON, J., Johnson M. S., Šali A., and Blundell T. L.
Proceedings of the Royal Society of London. Series B: Biological Sciences. Volume 241, Number 1301, (1990), p.132
The three-dimensional structure and evolution of HIV-I protease
Wilderspin, A., Gaskin D., Lapatto R., Blundell T. L., Hemmings A., OVERINGTON J., Pitts J., Wood S., HU Z. Z., Pearl L., et al.
Retroviral Proteases. (1990), p.79–91
Knowledge-based protein modelling: human plasma kallikrein and human neutrophil defensin
Johnson, M. S., OVERINGTON J. P., and Šali A.
Current Research in Protein Chemistry: Techniques, Structure and Function. (1990), p.567–574
From comparisons of protein sequences and structures to protein modelling and design
? ali, A., OVERINGTON J. P., Johnson M. S., and Blundell T. L.
Trends in Biochemical Sciences. Volume 15, Number 6, (1990), p.235–240
Three-dimensional structure of a B-type chymopapain.
Topham, C. M., OVERINGTON J., O'Driscoll M., Salih E., Thomas M., Thomas EW, and Brocklehurst K.
Biochemical Society Transactions. Volume 18, Number 5, (1990), p.933
Investigation of mechanistic consequences of natural structural variation within the cysteine proteinases by knowledge-based modelling and kinetic methods
Topham, C. M., OVERINGTON J., Kowlessur D., Thomas M., Thomas EW, and Brocklehurst K.
Biochemical Society Transactions. Volume 18, (1990), p.579–580
Three-dimensional structure and thiol reactivity characteristics of chymopapain M (papaya proteinase IV)
Topham, C. M., OVERINGTON J., Thomas M., Kowlessur D., Thomas EW, and Brocklehurst K.
Biochemical Society Transactions. Volume 18, (1990), p.934–935
Knowledge-based protein modeling and the design of novel molecules
Blundell, T. L., Johnson M. S., OVERINGTON J. P., and Šali A.
(1990),
An assessment of COMPOSER: a rule-based approach to modelling protein structure.
Topham, C. M., Thomas P., OVERINGTON J. P., Johnson M. S., Eisenmenger F., Blundell T. L., and others
Biochemical Society symposium. Volume 57, (1990), p.1
From comparisons of protein sequences and structures to protein modelling and design
Šali, A., OVERINGTON J. P., Johnson M. S., and Blundell T. L.
Trends in Biochemical Sciences. Volume 15, Number 6, (1990), p.235–240
From the comparative analysis of proteins to knowledge based modeling
Johnson, M. S., OVERINGTON J., Šali A., Thomas P., and Blundell T. L.
Journal of Molecular Graphics. Volume 8, Number 4, (1990), p.231–231
Structure and engineering of proteins: New developments
Johnson, M. S., OVERINGTON J., Šali A., HU Z. Z., Donnelly D., Thomas P., McCleod A., Goold R., Topham C., Blundell T. L., et al.
Fresenius' Journal of Analytical Chemistry. Volume 337, Number 1, (1990), p.1–3
Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure
OVERINGTON, J., Johnson M., Topham C., McLeod A., Šali A., HU Z. Z., Sibanda L., and Blunckll T.
Current science. Volume 59, Number 17Л, (1990), p.18–25

1989

Protein engineering and design
Blundell, T. L., Elliott G., Gardner SP, Hubbard T., Islam S., Johnson M., Mantafounis D., Murray-Rust P., OVERINGTON J., Pitts JE, et al.
Philosophical Transactions of the Royal Society of London. B, Biological Sciences. Volume 324, Number 1224, (1989), p.447–460
X-ray analysis of HIV-1 proteinase at 2.7A resolution confirms structural homology among retroviral enzymes
Lapatto, R., Blundell T., Hemmings A., OVERINGTON J., Wilderspin A., Wood S., Merson J. R., Whittle P. J., Danley D. E., Geoghegan K. F., et al.
(1989),

1988

The knowledge-based modelling of tissue-type plasminogen activator and its interactions with its inhibitor endothelial cell plasminogen activator inhibitor
OVERINGTON, J. P., Sutcliffe MJ, Watson F., James K., Campbell S., and Blundell T. L.
Proceedings of the 8th International Biotechnology Symposium. (1988), p.279–304
Knowledge-based protein modelling and design
Blundell, T., Carney D., Gardner S., Hayes F., Howlin B., Hubbard T., OVERINGTON J., Singh D. A., Sibanda B. L., and Sutcliffe M.
European Journal of Biochemistry. Volume 172, Number 3, (1988), p.513–520