Publications

2014

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

Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling.
van Westen GJ, Bender A, Overington JP.
J Chem Biol Volume 7 (2014) p.119-123

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.
Kruger FA, Gaulton A, Nowotka M, Overington JP.
Bioinformatics Volume (2014) p.

'Big data' in pharmaceutical science: challenges and opportunities.
Dossetter AG, Ecker G, Laverty H, Overington J.
Future Med Chem Volume 6 (2014) p.857-864

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 ChEMBL database: a taster for medicinal chemists.
Papadatos G, Overington JP.
Future Med Chem Volume 6 (2014) p.361-364

Transporter assays and assay ontologies: useful tools for drug discovery.
Zdrazil B, Chichester C, Zander Balderud L, Engkvist O, Gaulton A, Overington JP.
Drug Discov Today Technol Volume 12 (2014) p.e47-54

Antibody informatics for drug discovery.
Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K.
Biochim Biophys Acta Volume 1844 (2014) p.2002-2015

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

An atlas of genetic influences on human blood metabolites.
Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, Arnold M, Erte I, Forgetta V, Yang TP, Walter K, Menni C, Chen L, Vasquez L, Valdes AM, Hyde CL, Wang V, Ziemek D, Roberts P, Xi L, Grundberg E, Multiple Tissue Human Expression Resource (MuTHER) Consortium, Waldenberger M, Richards JB, Mohney RP, Milburn MV, John SL, Trimmer J, Theis FJ, Overington JP, Suhre K, Brosnan MJ, Gieger C, Kastenmüller G, Spector TD, Soranzo N.
Nat Genet Volume 46 (2014) p.543-550

diXa: a Data Infrastructure for Chemical Safety Assessment.
Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JC.
Bioinformatics Volume (2014) p.

A document classifier for medicinal chemistry publications trained on the ChEMBL corpus.
Papadatos G, van Westen GJ, Croset S, Santos R, Trubian S, Overington JP.
J Cheminform Volume 6 (2014) p.40

UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers.
Chambers J, Davies M, Gaulton A, Papadatos G, Hersey A, Overington JP.
J Cheminform Volume 6 (2014) p.43

A community computational challenge to predict the activity of pairs of compounds.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community.
Nat Biotechnol Volume 32 (2014) p.1213-1222

A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-Ud-Din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G, NCI DREAM Community.
Nat Biotechnol Volume 32 (2014) p.1202-1212

Structural studies of adipokinetic hormones in water and DPC micelle solution using NMR distance restrained molecular dynamics.
Jackson GE, Gamieldien R, Mugumbate G, Gäde G.
Peptides Volume 53 (2014) p.270-277

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

2013

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

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

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

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

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

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

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

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

Anopheles gambiae, Anoga-HrTH hormone, free and bound structure--a nuclear magnetic resonance experiment.
Mugumbate G, Jackson GE, van der Spoel D, Kövér KE, Szilágyi L.
Peptides Volume 41 (2013) p.94-100

Tetrazole-based deoxyamodiaquines: synthesis, ADME/PK profiling and pharmacological evaluation as potential antimalarial agents.
Tukulula M, Njoroge M, Mugumbate GC, Gut J, Rosenthal PJ, Barteau S, Streckfuss J, Heudi O, Kameni-Tcheudji J, Chibale K.
Bioorg Med Chem Volume 21 (2013) p.4904-4913

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

Drug metabolite generation using a laboratory evolved NADPH independent cytochrome P450: application of in vitro and in silico approaches.
Chigorimbo-Murefu NT, Njoroge M, Louw S, Mugumbate G, Chibale K.
Drug Metab Lett Volume 7 (2013) p.68-77

Novel anti-plasmodial hits identified by virtual screening of the ZINC database.
Mugumbate G, Newton AS, Rosenthal PJ, Gut J, Moreira R, Chibale K, Guedes RC.
J Comput Aided Mol Des Volume 27 (2013) p.859-871

2012

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

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

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

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

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

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

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

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

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

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

2011

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

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

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

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

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

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

2010

Role of open chemical data in aiding drug discovery and design.
Gaulton A, Overington JP.
Future Med Chem Volume 2 (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, Perišić O, Wass J, Bento AP, Overington J, Al-Lazikani B, Johnson ME.
Drug Discov Today Volume 15 (2010) p.804-811

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

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

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

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