Publications

2014

The ChEMBL bioactivity database: an update.
Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP.
Nucleic Acids Res Volume 42 (2014) p.d1083-90

The functional therapeutic chemical classification system.
Croset S, Overington JP, Rebholz-Schuhmann D.
Bioinformatics Volume 30 (2014) p.876-883

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.
Ochoa R, Davies M, Papadatos G, Atkinson F, Overington JP.
Bioinformatics Volume 30 (2014) p.298-300

Chemical, target, and bioactive properties of allosteric modulation.
van Westen GJ, Gaulton A, Overington JP.
PLoS Comput Biol Volume 10 (2014) p.e1003559

2013

Brain: biomedical knowledge manipulation.
Croset S, Overington JP, Rebholz-Schuhmann D.
Bioinformatics Volume 29 (2013) p.1238-1239

Structure-based identification of OATP1B1/3 inhibitors.
De Bruyn T, van Westen GJ, Ijzerman AP, Stieger B, de Witte P, Augustijns PF, Annaert PP.
Mol Pharmacol Volume 83 (2013) p.1257-1267

UniChem: a unified chemical structure cross-referencing and identifier tracking system.
Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP.
J Cheminform Volume 5 (2013) p.3

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic Acids Res Volume 41 (2013) p.d773-80

Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data.
van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.
PLoS Comput Biol Volume 9 (2013) p.e1002899

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.
Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.
PLoS Comput Biol Volume 9 (2013) p.e1003253

A ligand's-eye view of protein similarity.
van Westen GJ, Overington JP.
Nat Methods Volume 10 (2013) p.116-117

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets.
van Westen GJ, Swier RF, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.
J Cheminform Volume 5 (2013) p.41

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A.
J Cheminform Volume 5 (2013) p.42

2012

Annotating Human P-Glycoprotein Bioassay Data.
Zdrazil B, Pinto M, Vasanthanathan P, Williams AJ, Balderud LZ, Engkvist O, Chichester C, Hersey A, Overington JP, Ecker GF.
Mol Inform Volume 31 (2012) p.599-609

Global analysis of small molecule binding to related protein targets.
Kruger FA, Overington JP.
PLoS Comput Biol Volume 8 (2012) p.e1002333

ChEMBL: a large-scale bioactivity database for drug discovery.
Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP.
Nucleic Acids Res Volume 40 (2012) p.d1100-7

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data.
van Westen GJ, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.
J Med Chem Volume 55 (2012) p.7010-7020

Mapping small molecule binding data to structural domains.
Kruger FA, Rostom R, Overington JP.
BMC Bioinformatics Volume 13 Suppl 17 (2012) p.s11

Cheminformatics
Wegner JK, Sterling A, Guha R, Bender A, Faulon J-L, Hastings J, O'Boyle N, Overington J, Van Vlijmen H, Willighagen E.
Commun ACM Volume 55 (2012) p.65-75

Toxicogenomics Investigation Under the eTOX Project
Taboureau O, Hersey A, Audouze K, Gautier L, Jacobsen UP, Akhtar R, Atkinson F, Overington JP, Brunak S.
J Pharmacogenomics Pharmacoproteomics Volume S7 (2012) p.1-5

A novel nonribose agonist, LUF5834, engages residues that are distinct from those of adenosine-like ligands to activate the adenosine A(2a) receptor.
Lane JR, Klein Herenbrink C, van Westen GJ, Spoorendonk JA, Hoffmann C, IJzerman AP.
Mol Pharmacol Volume 81 (2012) p.475-487

Open data for drug discovery: learning from the biological community.
Hersey A, Senger S, Overington JP.
Future Med Chem Volume 4 (2012) p.1865-1867

Three "hotspots" important for adenosine A(2B) receptor activation: a mutational analysis of transmembrane domains 4 and 5 and the second extracellular loop.
Peeters MC, Li Q, van Westen GJ, Ijzerman AP.
Purinergic Signal Volume 8 (2012) p.23-38

2011

Collation and data-mining of literature bioactivity data for drug discovery.
Bellis LJ, Akhtar R, Al-Lazikani B, Atkinson F, Bento AP, Chambers J, Davies M, Gaulton A, Hersey A, Ikeda K, Krüger FA, Light Y, McGlinchey S, Santos R, Stauch B, Overington JP.
Biochem Soc Trans Volume 39 (2011) p.1365-1370

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, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.
Nat Rev Drug Discov Volume 10 (2011) p.661-669

Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space.
van der Horst E, Peironcely JE, van Westen GJ, van den Hoven OO, Galloway WR, Spring DR, Wegner JK, van Vlijmen HW, Ijzerman AP, Overington JP, Bender A.
Curr Top Med Chem Volume 11 (2011) p.1964-1977

Rapid analysis of pharmacology for infectious diseases.
Hopkins AL, Bickerton GR, Carruthers IM, Boyer SK, Rubin H, Overington JP.
Curr Top Med Chem Volume 11 (2011) p.1292-1300

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
Nat Methods Volume 8 (2011) p.528-529

Probing the links between in vitro potency, ADMET and physicochemical parameters.
Gleeson MP, Hersey A, Montanari D, Overington J.
Nat Rev Drug Discov Volume 10 (2011) p.197-208

2010

Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation.
Abad-Zapatero C, Perišić O, Wass J, Bento AP, Overington J, Al-Lazikani B, Johnson ME.
Drug Discov Today Volume 15 (2010) p.804-811

Role of open chemical data in aiding drug discovery and design.
Gaulton A, Overington JP.
Future Med Chem Volume 2 (2010) p.903-907

2009

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr.
Overington J.
J Comput Aided Mol Des Volume 23 (2009) p.195-198

New open drug activity data at EBI
Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J.
Chemistry Central Journal Volume 3 (2009) p.o3

The genome of the blood fluke Schistosoma mansoni.
Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM.
Nature Volume 460 (2009) p.352-358

2008

Genomic-scale prioritization of drug targets: the TDR Targets database.
Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL.
Nat Rev Drug Discov Volume 7 (2008) p.900-907