Janet Thornton

Janet Thornton

Director Emeritus of EMBL-EBI and Senior Scientist

Professor Dame Janet Thornton was Director of EMBL-EBI from October 2001 to June 2015, and played a key role in ELIXIR, the pan-European infrastructure for biological data, since its inception. Her research group focuses on understanding protein structure, function and evolution using computational approaches. After a physics degree she completed her PhD at the UK NIMR before post doctoral studies at Oxford. She then held a joint appointment at University College London and the Bernal Chair in the Crystallography Department at Birkbeck College. Professor Thornton is a Fellow of the Royal Society, a Fellow of the Academy of Medical Sciences, a member of EMBO and a foreign associate of the US National Academy of Sciences.

ORCID iD: 0000-0003-0824-4096

Tel:+44 (0)1223 494 648 / Fax:+44 (0)1223 494 496

Research

Find out about research activity in the Thornton research group

Thornton projects

Building data bridges from biology to medicine in Europe

BioMedBridges is a joint effort of ten biomedical sciences research infrastructures on the ESFRI roadmap. Together, the project partners will develop the shared e-infrastructure—the technical bridges—to allow interoperability between data and services in the biological, medical, translational and clinical domains and thus strengthen biomedical resources in Europe. Launched in January 2012, BioMedBridges is a four-year initiative funded with €10.6 million by the European Commission under the Seventh Framework Programme.

Professor Dame Janet Thornton coordinates the BioMedBridges project at EMBL-EBI, on behalf of ELIXIR. Full time BioMedBridges staff, workpackage leaders and other contributors to the project are listed here. To learn more about BioMedBridges, visit the website or contact Stephanie Suhr, BioMedBridges Project Manager.

Publications

2015

CATH: comprehensive structural and functional annotations for genome sequences.
Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA.
Nucleic Acids Res Volume 43 (2015) p.d376-81
DOI: 10.1093/nar/gku947

2014

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
Nucleic Acids Res Volume 42 (2014) p.d485-9
DOI: 10.1093/nar/gkt1243

Exploring the biological and chemical complexity of the ligases.
Holliday GL, Rahman SA, Furnham N, Thornton JM.
J Mol Biol Volume 426 (2014) p.2098-2111
DOI: 10.1016/j.jmb.2014.03.008

The NAD Binding Domain and the Short Chain Dehydrogenase/Reductase (SDR) Superfamily
Furnham N, Holliday GL, Thornton JM.
Volume (2014) p.191

PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA.
Nucleic Acids Res Volume 42 (2014) p.d292-6
DOI: 10.1093/nar/gkt940

DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.
Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D.
PLoS Genet Volume 10 (2014) p.e1004109
DOI: 10.1371/journal.pgen.1004109

Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM.
Nat Methods Volume 11 (2014) p.171-174

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
Papatheodorou I, Petrovs R, Thornton JM.
Bioinformatics Volume 30 (2014) p.2999-3003
DOI: 10.1093/bioinformatics/btu493

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.
Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D.
Aging (Albany NY) Volume 6 (2014) p.98-117

EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.
Nat Methods Volume 11 (2014) p.171-174
DOI: 10.1038/nmeth.2803

The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.
Curr Opin Struct Biol Volume 26 (2014) p.121-130
DOI: 10.1016/j.sbi.2014.06.002

2013

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Ziehm M, Piper MD, Thornton JM.
Aging Cell Volume 12 (2013) p.917-922
DOI: 10.1111/acel.12123

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
Ziehm M, Thornton JM.
Aging Cell Volume 12 (2013) p.910-916
DOI: 10.1111/acel.12121

Protein Data Resources
Furnham N, Garavelli JS, Thornton JM.
Volume (2013) p.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM.
Acta Crystallogr D Biol Crystallogr Volume 69 (2013) p.2395-2402
DOI: 10.1107/s0907444913022294

Abstracting knowledge from the protein data bank.
Furnham N, Laskowski RA, Thornton JM.
Biopolymers Volume 99 (2013) p.183-188
DOI: 10.1002/bip.22107

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.
Nucleic Acids Res Volume 41 (2013) p.d490-8
DOI: 10.1093/nar/gks1211

The Ramachandran Plot and Protein Structure Validation
Laskowski RA, Furnham N, Thornton JM.
Volume (2013) p.62-75

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
DOI: 10.1093/nar/gks1112

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM.
PLoS Comput Biol Volume 9 (2013) p.e1003382
DOI: 10.1371/journal.pcbi.1003382

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM.
Mol Biosyst Volume 9 (2013) p.1756-1764
DOI: 10.1039/c3mb25485b

Elucidating human phosphatase-substrate networks.
Li X, Wilmanns M, Thornton J, Köhn M.
Sci Signal Volume 6 (2013) p.rs10
DOI: 10.1126/scisignal.2003203

2012

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM.
Nucleic Acids Res Volume 40 (2012) p.d776-82
DOI: 10.1093/nar/gkr852

Efficient photocatalytic hydrogen production by platinum-loaded carbon-doped cadmium indate nanoparticles.
Thornton JM, Raftery D.
ACS Appl Mater Interfaces Volume 4 (2012) p.2426-2431
DOI: 10.1021/am300093t

Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Schwarz MA, Thornton J, Xu H, Awasthi N, Schwarz RE.
PLoS One Volume 7 (2012) p.e33101
DOI: 10.1371/journal.pone.0033101

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM.
PLoS One Volume 7 (2012) p.e50881
DOI: 10.1371/journal.pone.0050881

Delivering ICT Infrastructure for Biomedical Research
Nyronen TH, Laitinen J, Tourunen O, Sternkopf D, Laurikainen R, Oster P, Lehtovuori PT, Miettinen TA, Simonen T, Perheentupa T, Vastrik I, Kallioniemi O, Lyall A, Thornton JM.
Volume (2012) p.37-44

Current challenges in genome annotation through structural biology and bioinformatics.
Furnham N, de Beer TA, Thornton JM.
Curr Opin Struct Biol Volume 22 (2012) p.594-601
DOI: 10.1016/j.sbi.2012.07.005

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM.
PLoS Comput Biol Volume 8 (2012) p.e1002403
DOI: 10.1371/journal.pcbi.1002403

Women in science.
Dean C, Osborn M, Oshlack A, Thornton J.
Genome Biol Volume 13 (2012) p.148
DOI: 10.1186/gb-2012-13-3-148

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, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J.
Nat Rev Drug Discov Volume 11 (2012) p.730
DOI: 10.1038/nrd3503-c2

ELIXIR: a distributed infrastructure for European biological data.
Crosswell LC, Thornton JM.
Trends Biotechnol Volume 30 (2012) p.241-242
DOI: 10.1016/j.tibtech.2012.02.002

2011

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.
Alic N, Andrews TD, Giannakou ME, Papatheodorou I, Slack C, Hoddinott MP, Cochemé HM, Schuster EF, Thornton JM, Partridge L.
Mol Syst Biol Volume 7 (2011) p.502
DOI: 10.1038/msb.2011.36

1,000 structures and more from the MCSG.
Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA.
BMC Struct Biol Volume 11 (2011) p.2
DOI: 10.1186/1472-6807-11-2

Celebrating structural biology.

Nat Struct Mol Biol Volume 18 (2011) p.1304-1316
DOI: 10.1038/nsmb1211-1304

The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P, Köhn M.
Biochemistry Volume 50 (2011) p.7579-7590
DOI: 10.1021/bi201095z

The new science of ageing.
Partridge L, Thornton J, Bates G.
Philos Trans R Soc Lond B Biol Sci Volume 366 (2011) p.6-8
DOI: 10.1098/rstb.2010.0298

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
DOI: 10.1038/nrd3503

Computational biology for ageing.
Wieser D, Papatheodorou I, Ziehm M, Thornton JM.
Philos Trans R Soc Lond B Biol Sci Volume 366 (2011) p.51-63
DOI: 10.1098/rstb.2010.0286

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
Holliday GL, Fischer JD, Mitchell JB, Thornton JM.
FEBS J Volume 278 (2011) p.3835-3845
DOI: 10.1111/j.1742-4658.2011.08190.x

Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA.
Nucleic Acids Res Volume 39 (2011) p.d420-6
DOI: 10.1093/nar/gkq1001

2010

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM.
Proteins Volume 78 (2010) p.1120-1136
DOI: 10.1002/prot.22633

The CoFactor database: organic cofactors in enzyme catalysis.
Fischer JD, Holliday GL, Thornton JM.
Bioinformatics Volume 26 (2010) p.2496-2497
DOI: 10.1093/bioinformatics/btq442

Domain-ligand mapping for enzymes.
Bashton M, Thornton JM.
J Mol Recognit Volume 23 (2010) p.194-208
DOI: 10.1002/jmr.992

Heme proteins--diversity in structural characteristics, function, and folding.
Smith LJ, Kahraman A, Thornton JM.
Proteins Volume 78 (2010) p.2349-2368
DOI: 10.1002/prot.22747

The structures and physicochemical properties of organic cofactors in biocatalysis.
Fischer JD, Holliday GL, Rahman SA, Thornton JM.
J Mol Biol Volume 403 (2010) p.803-824
DOI: 10.1016/j.jmb.2010.09.018

The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J.
Nucleic Acids Res Volume 38 (2010) p.d17-25
DOI: 10.1093/nar/gkp986

The (non)malignancy of cancerous amino acidic substitutions.
Talavera D, Taylor MS, Thornton JM.
Proteins Volume 78 (2010) p.518-529
DOI: 10.1002/prot.22574

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.
Slack C, Werz C, Wieser D, Alic N, Foley A, Stocker H, Withers DJ, Thornton JM, Hafen E, Partridge L.
PLoS Genet Volume 6 (2010) p.e1000881
DOI: 10.1371/journal.pgen.1000881

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.
Schuster E, McElwee JJ, Tullet JM, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D.
Mol Syst Biol Volume 6 (2010) p.399
DOI: 10.1038/msb.2010.54

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M.
Proc Natl Acad Sci U S A Volume 107 (2010) p.4135-4140
DOI: 10.1073/pnas.0910632107

2009

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
DOI: 10.1186/1752-153x-3-s1-o3

Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday GL, Mitchell JB, Thornton JM.
J Mol Biol Volume 390 (2009) p.560-577
DOI: 10.1016/j.jmb.2009.05.015

The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ.
Biochem Soc Trans Volume 37 (2009) p.723-726
DOI: 10.1042/bst0370723

Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network.
Genome Biol Volume 10 (2009) p.401
DOI: 10.1186/gb-2009-10-2-401

Protein promiscuity and its implications for biotechnology.
Nobeli I, Favia AD, Thornton JM.
Nat Biotechnol Volume 27 (2009) p.157-167
DOI: 10.1038/nbt1519

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM.
J Mol Biol Volume 388 (2009) p.356-380
DOI: 10.1016/j.jmb.2009.02.052

Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I.
J Chem Inf Model Volume 49 (2009) p.2272-2289
DOI: 10.1021/ci900196u

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U.
Chem Biol Interact Volume 178 (2009) p.94-98
DOI: 10.1016/j.cbi.2008.10.040

Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.
J Cheminform Volume 1 (2009) p.12
DOI: 10.1186/1758-2946-1-12

WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM.
Bioinformatics Volume 25 (2009) p.1192-1194
DOI: 10.1093/bioinformatics/btp116

Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M, Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, Thomas G, Carling D, Okkenhaug K, Thornton JM, Partridge L, Gems D, Withers DJ.
Science Volume 326 (2009) p.140-144
DOI: 10.1126/science.1177221

Protein Evolution – Sequence, Structure and Systems
Sternberg M, Thornton J, Laskowski R.
Volume (2009) p.52

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva R, Thornton JM, Pellegrini-Calace M.
Bioinformatics Volume 25 (2009) p.3183-3184
DOI: 10.1093/bioinformatics/btp545

Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Watson JD, Thornton JM.
Volume (2009) p.201-215
DOI: 10.1007/978-90-481-2339-1_13

The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM.
FEBS Lett Volume 583 (2009) p.1692-1698
DOI: 10.1016/j.febslet.2009.03.019

Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM.
J R Soc Interface Volume 6 (2009) p.129-147
DOI: 10.1098/rsif.2008.0341

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA.
Nucleic Acids Res Volume 37 (2009) p.d310-4
DOI: 10.1093/nar/gkn877

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace M, Maiwald T, Thornton JM.
PLoS Comput Biol Volume 5 (2009) p.e1000440
DOI: 10.1371/journal.pcbi.1000440

Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM.
Nat Chem Biol Volume 5 (2009) p.521-525
DOI: 10.1038/nchembio0809-521

Enhanced DNA binding capacity on up-regulated epidermal wild-type p53 in vitiligo by H2O2-mediated oxidation: a possible repair mechanism for DNA damage.
Salem MM, Shalbaf M, Gibbons NC, Chavan B, Thornton JM, Schallreuter KU.
FASEB J Volume 23 (2009) p.3790-3807
DOI: 10.1096/fj.09-132621

The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C.
Structure Volume 17 (2009) p.1051-1062
DOI: 10.1016/j.str.2009.06.015

Metal-MACiE: a database of metals involved in biological catalysis.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
Bioinformatics Volume 25 (2009) p.2088-2089
DOI: 10.1093/bioinformatics/btp256

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.
PLoS Comput Biol Volume 5 (2009) p.e1000585
DOI: 10.1371/journal.pcbi.1000585

Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.
Nature Volume 461 (2009) p.168-170
DOI: 10.1038/461168a

Protein function annotation by homology-based inference.
Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A.
Genome Biol Volume 10 (2009) p.207
DOI: 10.1186/gb-2009-10-2-207

2008

Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
Selman C, Lingard S, Choudhury AI, Batterham RL, Claret M, Clements M, Ramadani F, Okkenhaug K, Schuster E, Blanc E, Piper MD, Al-Qassab H, Speakman JR, Carmignac D, Robinson IC, Thornton JM, Gems D, Partridge L, Withers DJ.
FASEB J Volume 22 (2008) p.807-818
DOI: 10.1096/fj.07-9261com

Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM.
Nat Rev Genet Volume 9 (2008) p.141-151
DOI: 10.1038/nrg2273

Evolution of binding sites for zinc and calcium ions playing structural roles.
Torrance JW, Macarthur MW, Thornton JM.
Proteins Volume 71 (2008) p.813-830
DOI: 10.1002/prot.21741

Methods to Characterize the Structure of Enzyme Binding Sites
Kahraman A and Thornton JM.
Volume (2008) p.189-221

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD, Nobeli I, Glaser F, Thornton JM.
J Mol Biol Volume 375 (2008) p.855-874
DOI: 10.1016/j.jmb.2007.10.065

Activation of the SPS amino acid-sensing pathway in Saccharomyces cerevisiae correlates with the phosphorylation state of a sensor component, Ptr3.
Liu Z, Thornton J, Spírek M, Butow RA.
Mol Cell Biol Volume 28 (2008) p.551-563
DOI: 10.1128/mcb.00929-07

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J.
Bioinformatics Volume 24 (2008) p.i105-11
DOI: 10.1093/bioinformatics/btn263

Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM.
BMC Evol Biol Volume 8 (2008) p.247
DOI: 10.1186/1471-2148-8-247

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.
Bioinformatics Volume 24 (2008) p.2767-2772
DOI: 10.1093/bioinformatics/btn528

Metal ions in biological catalysis: from enzyme databases to general principles.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
J Biol Inorg Chem Volume 13 (2008) p.1205-1218
DOI: 10.1007/s00775-008-0404-5

PROCOGNATE: a cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
Nucleic Acids Res Volume 36 (2008) p.d618-22
DOI: 10.1093/nar/gkm611

2007

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA.
Nucleic Acids Res Volume 35 (2007) p.d291-7
DOI: 10.1093/nar/gkl959

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM.
Nucleic Acids Res Volume 35 (2007) p.d515-20
DOI: 10.1093/nar/gkl774

The geometry of interactions between catalytic residues and their substrates.
Torrance JW, Holliday GL, Mitchell JB, Thornton JM.
J Mol Biol Volume 369 (2007) p.1140-1152
DOI: 10.1016/j.jmb.2007.03.055

Construction, visualisation, and clustering of transcription networks from microarray expression data.
Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ.
PLoS Comput Biol Volume 3 (2007) p.2032-2042
DOI: 10.1371/journal.pcbi.0030206

The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.
Proc Natl Acad Sci U S A Volume 104 (2007) p.5495-5500
DOI: 10.1073/pnas.0700800104

Towards fully automated structure-based function prediction in structural genomics: a case study.
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM.
J Mol Biol Volume 367 (2007) p.1511-1522
DOI: 10.1016/j.jmb.2007.01.063

Structural and chemical profiling of the human cytosolic sulfotransferases.
Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH.
PLoS Biol Volume 5 (2007) p.e97
DOI: 10.1371/journal.pbio.0050097

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM.
PLoS Comput Biol Volume 3 (2007) p.1993-2002
DOI: 10.1371/journal.pcbi.0030198

Evolutionary conservation of regulated longevity assurance mechanisms.
McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas JH, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D.
Genome Biol Volume 8 (2007) p.r132
DOI: 10.1186/gb-2007-8-7-r132

Correcting for sequence biases in present/absent calls.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome Biol Volume 8 (2007) p.r125
DOI: 10.1186/gb-2007-8-6-r125

Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
J Mol Biol Volume 368 (2007) p.283-301
DOI: 10.1016/j.jmb.2007.01.086

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM.
Bioinformatics Volume 23 (2007) p.e104-9
DOI: 10.1093/bioinformatics/btl292

Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome Biol Volume 8 (2007) p.r126
DOI: 10.1186/gb-2007-8-6-r126

Evolving Methods for Macromolecular Crystallography
Watson J, Golovin A, Laskowski R, Henrick K, Thornton JM, Joachimiak A and Edwards A.
Volume (2007) p.165-179

Evolution of enzymes and pathways for the biosynthesis of cofactors.
Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ.
Nat Prod Rep Volume 24 (2007) p.972-987
DOI: 10.1039/b703107f

Variation of geometrical and phsicochemical properties in protein binding pockets and their ligands
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
Volume (2007) p.

The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.
J Mol Biol Volume 372 (2007) p.1261-1277
DOI: 10.1016/j.jmb.2007.07.034

2006

Protein superfamily evolution and the last universal common ancestor (LUCA).
Ranea JA, Sillero A, Thornton JM, Orengo CA.
J Mol Evol Volume 63 (2006) p.513-525
DOI: 10.1007/s00239-005-0289-7

Erratum to "Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans" [Mech. Ageing Dev. 127 (5) (2006) 458-472].
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D.
Mech Ageing Dev Volume 127 (2006) p.922-936
DOI: 10.1016/j.mad.2006.10.002

Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
J Mol Biol Volume 364 (2006) p.836-852
DOI: 10.1016/j.jmb.2006.09.041

Integrating biological data through the genome.
Reeves GA, Thornton JM, BioSapiens Network of Excellence.
Hum Mol Genet Volume 15 Spec No 1 (2006) p.r81-7
DOI: 10.1093/hmg/ddl086

A method for localizing ligand binding pockets in protein structures.
Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.
Proteins Volume 62 (2006) p.479-488
DOI: 10.1002/prot.20769

Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans.
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D.
Mech Ageing Dev Volume 127 (2006) p.458-472
DOI: 10.1016/j.mad.2006.01.006

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Whamond GS, Thornton JM.
J Mol Biol Volume 359 (2006) p.238-247
DOI: 10.1016/j.jmb.2006.03.029

Introduction. Bioinformatics: from molecules to systems.
Jones DT, Sternberg MJ, Thornton JM.
Philos Trans R Soc Lond B Biol Sci Volume 361 (2006) p.389-391
DOI: 10.1098/rstb.2005.1811

A bioinformatician's view of the metabolome.
Nobeli I, Thornton JM.
Bioessays Volume 28 (2006) p.534-545
DOI: 10.1002/bies.20414

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.
Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM.
Genome Biol Volume 7 (2006) p.r89
DOI: 10.1186/gb-2006-7-10-r89

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM.
J Mol Biol Volume 356 (2006) p.928-944
DOI: 10.1016/j.jmb.2005.12.012

Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.
Selman C, Kerrison ND, Cooray A, Piper MD, Lingard SJ, Barton RH, Schuster EF, Blanc E, Gems D, Nicholson JK, Thornton JM, Partridge L, Withers DJ.
Physiol Genomics Volume 27 (2006) p.187-200
DOI: 10.1152/physiolgenomics.00084.2006

SPINE bioinformatics and data-management aspects of high-throughput structural biology.
Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K.
Acta Crystallogr D Biol Crystallogr Volume 62 (2006) p.1184-1195
DOI: 10.1107/s090744490602991x

2005

Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.
Pellegrini-Calace M, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.2129-2140
DOI: 10.1093/nar/gki349

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Laskowski RA, Chistyakov VV, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.d266-8
DOI: 10.1093/nar/gki001

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM.
Bioinformatics Volume 21 (2005) p.2347-2355
DOI: 10.1093/bioinformatics/bti337

Understanding nature's catalytic toolkit.
Gutteridge A, Thornton JM.
Trends Biochem Sci Volume 30 (2005) p.622-629
DOI: 10.1016/j.tibs.2005.09.006

Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression.
Giannattasio S, Liu Z, Thornton J, Butow RA.
J Biol Chem Volume 280 (2005) p.42528-42535
DOI: 10.1074/jbc.m509187200

Conformational changes observed in enzyme crystal structures upon substrate binding.
Gutteridge A, Thornton J.
J Mol Biol Volume 346 (2005) p.21-28
DOI: 10.1016/j.jmb.2004.11.013

Effective function annotation through catalytic residue conservation.
George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB.
Proc Natl Acad Sci U S A Volume 102 (2005) p.12299-12304
DOI: 10.1073/pnas.0504833102

Prediction of protein function from structure: insights from methods for the detection of local structural similarities.
Najmanovich RJ, Torrance JW, Thornton JM.
Biotechniques Volume 38 (2005) p.847, 849, 851

Protein families and their evolution-a structural perspective.
Orengo CA, Thornton JM.
Annu Rev Biochem Volume 74 (2005) p.867-900
DOI: 10.1146/annurev.biochem.74.082803.133029

Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1.
Ryan AW, Thornton JM, Brophy K, Daly JS, McLoughlin RM, O'Morain C, Abuzakouk M, Kennedy NP, Stevens FM, Feighery C, Kelleher D, McManus R.
Tissue Antigens Volume 65 (2005) p.150-155
DOI: 10.1111/j.1399-0039.2005.00354.x

A novel degron-mediated degradation of the RTG pathway regulator, Mks1p, by SCFGrr1.
Liu Z, Spírek M, Thornton J, Butow RA.
Mol Biol Cell Volume 16 (2005) p.4893-4904
DOI: 10.1091/mbc.e05-06-0516

Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
Shanahan HP, Thornton JM.
Biopolymers Volume 78 (2005) p.318-328
DOI: 10.1002/bip.20295

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
Ferrer-Costa C, Shanahan HP, Jones S, Thornton JM.
Bioinformatics Volume 21 (2005) p.3679-3680
DOI: 10.1093/bioinformatics/bti575

ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.w89-93
DOI: 10.1093/nar/gki414

The complement of enzymatic sets in different species.
Freilich S, Spriggs RV, George RA, Al-Lazikani B, Swindells M, Thornton JM.
J Mol Biol Volume 349 (2005) p.745-763
DOI: 10.1016/j.jmb.2005.04.027

Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM.
Genome Biol Volume 6 (2005) p.r56
DOI: 10.1186/gb-2005-6-7-r56

Binding Pocket Shape Analysis for Protein Function Prediction
Morris RJ, Kahraman A, Thornton JM.
Acta Crystallogr Volume D61 (2005) p.c156-c157

Predicting protein function from sequence and structural data.
Watson JD, Laskowski RA, Thornton JM.
Curr Opin Struct Biol Volume 15 (2005) p.275-284
DOI: 10.1016/j.sbi.2005.04.003

The European Bioinformatics Institute's data resources: towards systems biology.
Brooksbank C, Cameron G, Thornton J.
Nucleic Acids Res Volume 33 (2005) p.d46-53
DOI: 10.1093/nar/gki026

Microeconomic principles explain an optimal genome size in bacteria.
Ranea JA, Grant A, Thornton JM, Orengo CA.
Trends Genet Volume 21 (2005) p.21-25
DOI: 10.1016/j.tig.2004.11.014

Progress of structural genomics initiatives: an analysis of solved target structures.
Todd AE, Marsden RL, Thornton JM, Orengo CA.
J Mol Biol Volume 348 (2005) p.1235-1260
DOI: 10.1016/j.jmb.2005.03.037

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.
Nobeli I, Spriggs RV, George RA, Thornton JM.
J Mol Biol Volume 347 (2005) p.415-436
DOI: 10.1016/j.jmb.2005.01.061

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C.
Nucleic Acids Res Volume 33 (2005) p.d247-51
DOI: 10.1093/nar/gki024

Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.
Torrance JW, Bartlett GJ, Porter CT, Thornton JM.
J Mol Biol Volume 347 (2005) p.565-581
DOI: 10.1016/j.jmb.2005.01.044

MACiE: a database of enzyme reaction mechanisms.
Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB.
Bioinformatics Volume 21 (2005) p.4315-4316
DOI: 10.1093/bioinformatics/bti693

Protein function prediction using local 3D templates.
Laskowski RA, Watson JD, Thornton JM.
J Mol Biol Volume 351 (2005) p.614-626
DOI: 10.1016/j.jmb.2005.05.067

Morphological aspects of oligomeric protein structures.
Ponstingl H, Kabir T, Gorse D, Thornton JM.
Prog Biophys Mol Biol Volume 89 (2005) p.9-35
DOI: 10.1016/j.pbiomolbio.2004.07.010

2004

Software Engineering Challenges in Bioinformatics
Barker J, Thornton JM.
ICSE Volume (2004) p.12-16

The Proteome and the Metabolome: A Structural Perspective
Nobeli I, Thornton JM.
Volume (2004) p.526-533

SCOPEC: a database of protein catalytic domains.
George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB.
Bioinformatics Volume 20 Suppl 1 (2004) p.i130-6
DOI: 10.1093/bioinformatics/bth948

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
Porter CT, Bartlett GJ, Thornton JM.
Nucleic Acids Res Volume 32 (2004) p.d129-33
DOI: 10.1093/nar/gkh028

Searching for functional sites in protein structures.
Jones S, Thornton JM.
Curr Opin Chem Biol Volume 8 (2004) p.3-7
DOI: 10.1016/j.cbpa.2003.11.001

The European dimension for the mouse genome mutagenesis program.
Auwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M, Berns A, Bradley A, Brown S, Carmeliet P, Chambon P, Cox R, Davidson D, Davies K, Duboule D, Forejt J, Granucci F, Hastie N, de Angelis MH, Jackson I, Kioussis D, Kollias G, Lathrop M, Lendahl U, Malumbres M, von Melchner H, Müller W, Partanen J, Ricciardi-Castagnoli P, Rigby P, Rosen B, Rosenthal N, Skarnes B, Stewart AF, Thornton J, Tocchini-Valentini G, Wagner E, Wahli W, Wurst W.
Nat Genet Volume 36 (2004) p.925-927
DOI: 10.1038/ng0904-925

Ligand selectivity and competition between enzymes in silico.
Macchiarulo A, Nobeli I, Thornton JM.
Nat Biotechnol Volume 22 (2004) p.1039-1045
DOI: 10.1038/nbt999

An examination of the conservation of surface patch polarity for proteins.
Shanahan HP, Thornton JM.
Bioinformatics Volume 20 (2004) p.2197-2204
DOI: 10.1093/bioinformatics/bth218

Haplotype variation at the IBD5/SLC22A4 locus (5q31) in coeliac disease in the Irish population.
Ryan AW, Thornton JM, Brophy K, Daly JS, O'Morain C, McLoughlin RM, Kennedy NP, Abuzakouk M, Stevens FM, Feighery C, Kelleher D, McManus R.
Tissue Antigens Volume 64 (2004) p.195-198
DOI: 10.1111/j.1399-0039.2004.00251.x

A practical and robust sequence search strategy for structural genomics target selection.
Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA.
Bioinformatics Volume 20 (2004) p.2288-2295
DOI: 10.1093/bioinformatics/bth240

Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
Shanahan HP, Garcia MA, Jones S, Thornton JM.
Nucleic Acids Res Volume 32 (2004) p.4732-4741
DOI: 10.1093/nar/gkh803

Evolution of protein superfamilies and bacterial genome size.
Ranea JA, Buchan DW, Thornton JM, Orengo CA.
J Mol Biol Volume 336 (2004) p.871-887
DOI: 10.1016/j.jmb.2003.12.044

Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
Eyre TA, Partridge L, Thornton JM.
Protein Eng Des Sel Volume 17 (2004) p.613-624
DOI: 10.1093/protein/gzh072

Toward the detection and validation of repeats in protein structure.
Murray KB, Taylor WR, Thornton JM.
Proteins Volume 57 (2004) p.365-380
DOI: 10.1002/prot.20202

Conformational change in substrate binding, catalysis and product release: an open and shut case?
Gutteridge A, Thornton J.
FEBS Lett Volume 567 (2004) p.67-73
DOI: 10.1016/j.febslet.2004.03.067

2003

The CATH database: an extended protein family resource for structural and functional genomics.
Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA.
Nucleic Acids Res Volume 31 (2003) p.452-455
DOI: 10.1093/nar/gkg062

Molecular basis of inherited diseases: a structural perspective.
Steward RE, MacArthur MW, Laskowski RA, Thornton JM.
Trends Genet Volume 19 (2003) p.505-513
DOI: 10.1016/s0168-9525(03)00195-1

Recognizing the fold of a protein structure.
Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C.
Bioinformatics Volume 19 (2003) p.1748-1759
DOI: 10.1093/bioinformatics/btg240

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Barker JA, Thornton JM.
Bioinformatics Volume 19 (2003) p.1644-1649
DOI: 10.1093/bioinformatics/btg226

Catalysing new reactions during evolution: economy of residues and mechanism.
Bartlett GJ, Borkakoti N, Thornton JM.
J Mol Biol Volume 331 (2003) p.829-860
DOI: 10.1016/s0022-2836(03)00734-4

Structural characterisation and functional significance of transient protein-protein interactions.
Nooren IM, Thornton JM.
J Mol Biol Volume 325 (2003) p.991-1018
DOI: 10.1016/s0022-2836(02)01281-0

A structure-based anatomy of the E.coli metabolome.
Nobeli I, Ponstingl H, Krissinel EB, Thornton JM.
J Mol Biol Volume 334 (2003) p.697-719
DOI: 10.1016/j.jmb.2003.10.008

Diversity of protein-protein interactions.
Nooren IM, Thornton JM.
EMBO J Volume 22 (2003) p.3486-3492
DOI: 10.1093/emboj/cdg359

Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Gutteridge A, Bartlett GJ, Thornton JM.
J Mol Biol Volume 330 (2003) p.719-734
DOI: 10.1016/s0022-2836(03)00515-1

The Proteome and the Metabolome
Thornton JM, Nobeli I.
Biopolymers Volume 71 (2003) p.281

A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
Dawe JH, Porter CT, Thornton JM, Tabor AB.
Proteins Volume 52 (2003) p.427-435
DOI: 10.1002/prot.10421

Using structural motif templates to identify proteins with DNA binding function.
Jones S, Barker JA, Nobeli I, Thornton JM.
Nucleic Acids Res Volume 31 (2003) p.2811-2823
DOI: 10.1093/nar/gkg386

A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks.
Shepherd AJ, Gorse D, Thornton JM.
Proteins Volume 50 (2003) p.290-302
DOI: 10.1002/prot.10290

Sequences and topology.
Gerstein M, Thornton JM.
Curr Opin Struct Biol Volume 13 (2003) p.341-343
DOI: 10.1016/s0959-440x(03)00080-0

Analysis of metabolic networks using a pathway distance metric through linear programming.
Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG.
Metab Eng Volume 5 (2003) p.211-219
DOI: 10.1016/s1096-7176(03)00043-0

Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.
Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM.
J Biol Chem Volume 278 (2003) p.26039-26045
DOI: 10.1074/jbc.m303867200

Gene3D: structural assignments for the biologist and bioinformaticist alike.
Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA.
Nucleic Acids Res Volume 31 (2003) p.469-473
DOI: 10.1093/nar/gkg051

From protein structure to biochemical function?
Laskowski RA, Watson JD, Thornton JM.
J Struct Funct Genomics Volume 4 (2003) p.167-177
DOI: 10.1023/a:1026127927612

The CATH domain structure database.
Orengo CA, Pearl FM, Thornton JM.
Methods Biochem Anal Volume 44 (2003) p.249-271

Protein-DNA interactions: the story so far and a new method for prediction.
Jones S, Thornton JM.
Comp Funct Genomics Volume 4 (2003) p.428-431
DOI: 10.1002/cfg.303

Inferring protein function from structure.
Bartlett GJ, Todd AE, Thornton JM.
Methods Biochem Anal Volume 44 (2003) p.387-407

Proteomics: The Protein Complement of the Genome
Ponstingl H, Thornton JM.
The biochemist Volume 25 (2003) p.7-9

Target selection and determination of function in structural genomics.
Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM.
IUBMB Life Volume 55 (2003) p.249-255
DOI: 10.1080/1521654031000123385

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
Jones S, Shanahan HP, Berman HM, Thornton JM.
Nucleic Acids Res Volume 31 (2003) p.7189-7198
DOI: 10.1093/nar/gkg922

2002

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA.
Genome Res Volume 12 (2002) p.503-514
DOI: 10.1101/gr.213802

PROCHECK: Validation of Protein Structure Coordinates
Laskowski RA, MacArthur MW, Thornton JM.
Volume (2002) p.

Toward predicting protein topology: an approach to identifying beta hairpins.
de la Cruz X, Hutchinson EG, Shepherd A, Thornton JM.
Proc Natl Acad Sci U S A Volume 99 (2002) p.11157-11162
DOI: 10.1073/pnas.162376199

Sequence and structural differences between enzyme and nonenzyme homologs.
Todd AE, Orengo CA, Thornton JM.
Structure Volume 10 (2002) p.1435-1451
DOI: 10.1016/s0969-2126(02)00861-4

Quantifying the similarities within fold space.
Harrison A, Pearl F, Mott R, Thornton J, Orengo C.
J Mol Biol Volume 323 (2002) p.909-926
DOI: 10.1016/s0022-2836(02)00992-0

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Luscombe NM, Thornton JM.
J Mol Biol Volume 320 (2002) p.991-1009
DOI: 10.1016/s0022-2836(02)00571-5

Automatic Interence of Protein Quatenary Structure from Crystals
Ponstingl H, Kabir T, Thornton JM.
J Appl Crystallogr Volume 36 (2002) p.1116-1122

Wavelet transforms for the characterization and detection of repeating motifs.
Murray KB, Gorse D, Thornton JM.
J Mol Biol Volume 316 (2002) p.341-363
DOI: 10.1006/jmbi.2001.5332

The CCPN project: an interim report on a data model for the NMR community.
Fogh R, Ionides J, Ulrich E, Boucher W, Vranken W, Linge JP, Habeck M, Rieping W, Bhat TN, Westbrook J, Henrick K, Gilliland G, Berman H, Thornton J, Nilges M, Markley J, Laue E.
Nat Struct Biol Volume 9 (2002) p.416-418
DOI: 10.1038/nsb0602-416

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.
Rison SC, Teichmann SA, Thornton JM.
J Mol Biol Volume 318 (2002) p.911-932
DOI: 10.1016/s0022-2836(02)00140-7

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
Nagano N, Orengo CA, Thornton JM.
J Mol Biol Volume 321 (2002) p.741-765
DOI: 10.1016/s0022-2836(02)00649-6

Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein.
Martin AC, Facchiano AM, Cuff AL, Hernandez-Boussard T, Olivier M, Hainaut P, Thornton JM.
Hum Mutat Volume 19 (2002) p.149-164
DOI: 10.1002/humu.10032

RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast prion [URE3].
Sekito T, Liu Z, Thornton J, Butow RA.
Mol Biol Cell Volume 13 (2002) p.795-804
DOI: 10.1091/mbc.01-09-0473

Pathway evolution, structurally speaking.
Rison SC, Thornton JM.
Curr Opin Struct Biol Volume 12 (2002) p.374-382
DOI: 10.1016/s0959-440x(02)00331-7

Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
Steward RE, Thornton JM.
Proteins Volume 48 (2002) p.178-191
DOI: 10.1002/prot.10152

Proteins, Small Molecules and Networks
Nobeli I, Thornton JM.
Volume (2002) p.332-341

Analysis of catalytic residues in enzyme active sites.
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM.
J Mol Biol Volume 324 (2002) p.105-121
DOI: 10.1016/s0022-2836(02)01036-7

Plasticity of enzyme active sites.
Todd AE, Orengo CA, Thornton JM.
Trends Biochem Sci Volume 27 (2002) p.419-426
DOI: 10.1016/s0968-0004(02)02158-8

The CATH protein family database: a resource for structural and functional annotation of genomes.
Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM.
Proteomics Volume 2 (2002) p.11-21
DOI: 10.1002/1615-9861(200201)2:1<11::aid-prot11>3.3.co;2-k

2001

The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
Nagano N, Porter CT, Thornton JM.
Protein Eng Volume 14 (2001) p.845-855
DOI: 10.1093/protein/14.11.845

The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution.
Thornton JM.
Protein Sci Volume 10 (2001) p.3-11
DOI: 10.1110/ps.10.1.3

Protein-protein interfaces: analysis of amino acid conservation in homodimers.
Valdar WS, Thornton JM.
Proteins Volume 42 (2001) p.108-124
DOI: 10.1002/1097-0134(20010101)42:1<108::aid-prot110>3.3.co;2-f

Protein-RNA interactions: a structural analysis.
Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM.
Nucleic Acids Res Volume 29 (2001) p.943-954
DOI: 10.1093/nar/29.4.943

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
Luscombe NM, Laskowski RA, Thornton JM.
Nucleic Acids Res Volume 29 (2001) p.2860-2874
DOI: 10.1093/nar/29.13.2860

A rapid classification protocol for the CATH Domain Database to support structural genomics.
Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA.
Nucleic Acids Res Volume 29 (2001) p.223-227
DOI: 10.1093/nar/29.1.223

Playing with Proteins
Thornton JM.
Volume (2001) p.30-33

Evolution of function in protein superfamilies, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
J Mol Biol Volume 307 (2001) p.1113-1143
DOI: 10.1006/jmbi.2001.4513

Conservation helps to identify biologically relevant crystal contacts.
Valdar WS, Thornton JM.
J Mol Biol Volume 313 (2001) p.399-416
DOI: 10.1006/jmbi.2001.5034

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C.
J Mol Biol Volume 311 (2001) p.693-708
DOI: 10.1006/jmbi.2001.4912

Small-molecule metabolism: an enzyme mosaic.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C.
Trends Biotechnol Volume 19 (2001) p.482-486
DOI: 10.1016/s0167-7799(01)01813-3

On the molecular discrimination between adenine and guanine by proteins.
Nobeli I, Laskowski RA, Valdar WS, Thornton JM.
Nucleic Acids Res Volume 29 (2001) p.4294-4309
DOI: 10.1093/nar/29.21.4294

Evaluation of a Knowledge-Based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes
Nobeli I, Mitchell JM, Alex A, Thornton JM.
J Comput Chem Volume 22 (2001) p.673-688

From genome to function.
Thornton JM.
Science Volume 292 (2001) p.2095-2097
DOI: 10.1126/science.292.5524.2095

Structural genomics takes off.
Thornton J.
Trends Biochem Sci Volume 26 (2001) p.88-89
DOI: 10.1016/s0968-0004(00)01765-5

2000

Using the CATH domain database to assign structures and functions to the genome sequences.
Pearl F, Todd AE, Bray JE, Martin AC, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA.
Biochem Soc Trans Volume 28 (2000) p.269-275

Comparison of functional annotation schemes for genomes.
Rison SC, Hodgman TC, Thornton JM.
Funct Integr Genomics Volume 1 (2000) p.56-69
DOI: 10.1007/s101420000005

Assigning genomic sequences to CATH.
Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA.
Nucleic Acids Res Volume 28 (2000) p.277-282
DOI: 10.1093/nar/28.1.277

Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.
Jones S, Marin A, Thornton JM.
Protein Eng Volume 13 (2000) p.77-82
DOI: 10.1093/protein/13.2.77

From structure to function: approaches and limitations.
Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA.
Nat Struct Biol Volume 7 Suppl (2000) p.991-994
DOI: 10.1038/80784

Discriminating between homodimeric and monomeric proteins in the crystalline state.
Ponstingl H, Henrick K, Thornton JM.
Proteins Volume 41 (2000) p.47-57
DOI: 10.1002/1097-0134(20001001)41:1<47::aid-prot80>3.3.co;2-#

An overview of the structures of protein-DNA complexes.
Luscombe NM, Austin SE, Berman HM, Thornton JM.
Genome Biol Volume 1 (2000) p.reviews001
DOI: 10.1186/gb-2000-1-1-reviews001

Analysis and prediction of carbohydrate binding sites.
Taroni C, Jones S, Thornton JM.
Protein Eng Volume 13 (2000) p.89-98
DOI: 10.1093/protein/13.2.89

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.
Bray JE, Todd AE, Pearl FM, Thornton JM, Orengo CA.
Protein Eng Volume 13 (2000) p.153-165
DOI: 10.1093/protein/13.3.153

1999

Protein-DNA interactions: A structural analysis.
Jones S, van Heyningen P, Berman HM, Thornton JM.
J Mol Biol Volume 287 (1999) p.877-896
DOI: 10.1006/jmbi.1999.2659

Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?
MacArthur MW, Thornton JM.
Acta Crystallogr D Biol Crystallogr Volume 55 (1999) p.994-1004
DOI: 10.1107/s0907444999002231

Evolution of protein function, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
Curr Opin Chem Biol Volume 3 (1999) p.548-556
DOI: 10.1016/s1367-5931(99)00007-1

Protein folds, functions and evolution.
Thornton JM, Orengo CA, Todd AE, Pearl FM.
J Mol Biol Volume 293 (1999) p.333-342
DOI: 10.1006/jmbi.1999.3054

Factors limiting the performance of prediction-based fold recognition methods.
de la Cruz X, Thornton JM.
Protein Sci Volume 8 (1999) p.750-759
DOI: 10.1110/ps.8.4.750

Small subunit rRNA gene sequences of Aeromonas salmonicida subsp. smithia and Haemophilus piscium reveal pronounced similarities with A. salmonicida subsp. salmonicida.
Thornton JM, Austin DA, Austin B, Powell R.
Dis Aquat Organ Volume 35 (1999) p.155-158
DOI: 10.3354/dao035155

Three-dimensional structure analysis of PROSITE patterns.
Kasuya A, Thornton JM.
J Mol Biol Volume 286 (1999) p.1673-1691
DOI: 10.1006/jmbi.1999.2581

From protein structure to function.
Orengo CA, Todd AE, Thornton JM.
Curr Opin Struct Biol Volume 9 (1999) p.374-382
DOI: 10.1016/s0959-440x(99)80051-7

Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
Nagano N, Hutchinson EG, Thornton JM.
Protein Sci Volume 8 (1999) p.2072-2084
DOI: 10.1110/ps.8.10.2072

Prediction of the location and type of beta-turns in proteins using neural networks.
Shepherd AJ, Gorse D, Thornton JM.
Protein Sci Volume 8 (1999) p.1045-1055
DOI: 10.1110/ps.8.5.1045

Protein structural topology: Automated analysis and diagrammatic representation.
Westhead DR, Slidel TW, Flores TP, Thornton JM.
Protein Sci Volume 8 (1999) p.897-904
DOI: 10.1110/ps.8.4.897

Correlation of observed fold frequency with the occurrence of local structural motifs.
Salem GM, Hutchinson EG, Orengo CA, Thornton JM.
J Mol Biol Volume 287 (1999) p.969-981
DOI: 10.1006/jmbi.1999.2642

Software Tools for Protein Structure Analysis and Fold Classification
Thornton JM, Mitchie AD, Hutchinson EG, Laskowski RA, Orengo CA.
Volume (1999) p.

COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.
Harding SE, Horton JC, Jones S, Thornton JM, Winzor DJ.
Biophys J Volume 76 (1999) p.2432-2438
DOI: 10.1016/s0006-3495(99)77398-4

Motif-based searching in TOPS protein topology databases.
Gilbert D, Westhead D, Nagano N, Thornton J.
Bioinformatics Volume 15 (1999) p.317-326
DOI: 10.1093/bioinformatics/15.4.317

BLEEP - A Potential of Mean Force Describing Protein-Ligan Interactions: Generating the Potential
Mitchell JBO, Laskowski RA, Alex A, Thornton JM.
J Comput Chem Volume 20 (1999) p.11

DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.
Todd AE, Orengo CA, Thornton JM.
Protein Eng Volume 12 (1999) p.375-379
DOI: 10.1093/protein/12.5.375

Polymerase chain reaction (PCR)-based typing analysis of atypical isolates of the fish pathogen Aeromonas salmonicida.
Høie S, Dalsgaard I, Aase IL, Heum M, Thornton JM, Powell R.
Syst Appl Microbiol Volume 22 (1999) p.403-411

The CATH Database provides insights into protein structure/function relationships.
Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM.
Nucleic Acids Res Volume 27 (1999) p.275-279
DOI: 10.1093/nar/27.1.275

1998

Classifying a protein in the CATH database of domain structures.
Orengo CA, Martin AM, Hutchinson G, Jones S, Jones DT, Michie AD, Swindells MB, Thornton JM.
Acta Crystallogr D Biol Crystallogr Volume 54 (1998) p.1155-1167
DOI: 10.1107/s0907444998007501

Determinants of strand register in antiparallel beta-sheets of proteins.
Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN.
Protein Sci Volume 7 (1998) p.2287-2300
DOI: 10.1002/pro.5560071106

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).
Patel SU, Osborn R, Rees S, Thornton JM.
Biochemistry Volume 37 (1998) p.983-990
DOI: 10.1021/bi971747d

Iditis: protein structure database.
Gardner S, Thornton J.
Acta Crystallogr D Biol Crystallogr Volume 54 (1998) p.1071-1077
DOI: 10.1107/s0907444998007112

Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.
Zuccotto F, Martin AC, Laskowski RA, Thornton JM, Gilbert IH.
J Comput Aided Mol Des Volume 12 (1998) p.241-257
DOI: 10.1023/a:1016085005275

New tools and resources for analysing protein structures and their interactions.
Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou M, Thornton JM.
Acta Crystallogr D Biol Crystallogr Volume 54 (1998) p.1132-1138
DOI: 10.1107/s0907444998007318

Design, synthesis and structure of a zinc finger with an artificial beta-turn.
Viles JH, Patel SU, Mitchell JB, Moody CM, Justice DE, Uppenbrink J, Doyle PM, Harris CJ, Sadler PJ, Thornton JM.
J Mol Biol Volume 279 (1998) p.973-986
DOI: 10.1006/jmbi.1998.1764

1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.
Bloch C Jr, Patel SU, Baud F, Zvelebil MJ, Carr MD, Sadler PJ, Thornton JM.
Proteins Volume 32 (1998) p.334-349
DOI: 10.1002/(sici)1097-0134(19980815)32:3<334::aid-prot9>3.0.co;2-h

Domain assignment for protein structures using a consensus approach: characterization and analysis.
Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM.
Protein Sci Volume 7 (1998) p.233-242
DOI: 10.1002/pro.5560070202

Validation of protein models derived from experiment.
Laskowski RA, MacArthur MW, Thornton JM.
Curr Opin Struct Biol Volume 8 (1998) p.631-639
DOI: 10.1016/s0959-440x(98)80156-5

Protein folds and functions.
Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM.
Structure Volume 6 (1998) p.875-884
DOI: 10.1016/s0969-2126(98)00089-6

Contemporary approaches to protein structure classification.
Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM.
Bioessays Volume 20 (1998) p.884-891
DOI: 10.1002/(sici)1521-1878(199811)20:11<884::aid-bies3>3.3.co;2-8

PQS: a protein quaternary structure file server.
Henrick K, Thornton JM.
Trends Biochem Sci Volume 23 (1998) p.358-361
DOI: 10.1016/s0968-0004(98)01253-5

Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage.
Smith GP, Patel SU, Windass JD, Thornton JM, Winter G, Griffiths AD.
J Mol Biol Volume 277 (1998) p.317-332
DOI: 10.1006/jmbi.1997.1621

Pattern Search over the TOPS Protein Topology Database
Gilbert DR, Westhead DR, Hatton DC, Thornton JM.
Protein Data Bank Quarterly Newsletter Volume 85 (1998) p.7-9

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

J Mol Biol Volume 276 (1998) p.417-436

Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Milburn D, Laskowski RA, Thornton JM.
Protein Eng Volume 11 (1998) p.855-859
DOI: 10.1093/protein/11.10.855

Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
Hubbard SJ, Beynon RJ, Thornton JM.
Protein Eng Volume 11 (1998) p.349-359
DOI: 10.1093/protein/11.5.349

Characterization of atypical Aeromonas salmonicida by different methods.
Austin B, Austin DA, Dalsgaard I, Gudmundsdóttir BK, Høie S, Thornton JM, Larsen JL, O'Hici B, Powell R.
Syst Appl Microbiol Volume 21 (1998) p.50-64

An atlas of protein topology cartoons available on the World-Wide Web.
Westhead DR, Hatton DC, Thornton JM.
Trends Biochem Sci Volume 23 (1998) p.35-36
DOI: 10.1016/s0968-0004(97)01161-4

The Future of Bioinformatics
Thornton JM.
Volume (1998) p.30-31

Protein structure prediction.
Westhead DR, Thornton JM.
Curr Opin Biotechnol Volume 9 (1998) p.383-389
DOI: 10.1016/s0958-1669(98)80012-8

Evolution of the androgen receptor: structure-function implications.
Thornton JW, Kelley DB.
Bioessays Volume 20 (1998) p.860-869
DOI: 10.1002/(sici)1521-1878(199810)20:10<860::aid-bies12>3.0.co;2-s

1997

Non-randomness in side-chain packing: the distribution of interplanar angles.
Mitchell JB, Laskowski RA, Thornton JM.
Proteins Volume 29 (1997) p.370-380
DOI: 10.1002/(sici)1097-0134(199711)29:3<370::aid-prot10>3.3.co;2-9

Analysis of protein-protein interaction sites using surface patches.
Jones S, Thornton JM.
J Mol Biol Volume 272 (1997) p.121-132
DOI: 10.1006/jmbi.1997.1234

Assessment of comparative modeling in CASP2.
Martin AC, MacArthur MW, Thornton JM.
Proteins Volume Suppl 1 (1997) p.14-28
DOI: 10.1002/(sici)1097-0134(1997)1+<14::aid-prot4>3.3.co;2-f

Prediction of protein-protein interaction sites using patch analysis.
Jones S, Thornton JM.
J Mol Biol Volume 272 (1997) p.133-143
DOI: 10.1006/jmbi.1997.1233

Modelling protein unfolding: hen egg-white lysozyme.
Williams MA, Thornton JM, Goodfellow JM.
Protein Eng Volume 10 (1997) p.895-903
DOI: 10.1093/protein/10.8.895

CATH--a hierarchic classification of protein domain structures.
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM.
Structure Volume 5 (1997) p.1093-1108
DOI: 10.1016/s0969-2126(97)00260-8

Computational Approaches to Protein Ligand Interactions: Protein-heme Complexes
Karmirantzou MI, Thornton JM.
Volume (1997) p.264-279

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
Wallace AC, Borkakoti N, Thornton JM.
Protein Sci Volume 6 (1997) p.2308-2323
DOI: 10.1002/pro.5560061104

PDBsum: a Web-based database of summaries and analyses of all PDB structures.
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM.
Trends Biochem Sci Volume 22 (1997) p.488-490
DOI: 10.1016/s0968-0004(97)01140-7

Structures of N-termini of helices in proteins.
Doig AJ, MacArthur MW, Stapley BJ, Thornton JM.
Protein Sci Volume 6 (1997) p.147-155
DOI: 10.1002/pro.5560060117

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Luscombe NM, Laskowski RA, Thornton JM.
Nucleic Acids Res Volume 25 (1997) p.4940-4945
DOI: 10.1093/nar/25.24.4940

1996

Protein clefts in molecular recognition and function.
Laskowski RA, Luscombe NM, Swindells MB, Thornton JM.
Protein Sci Volume 5 (1996) p.2438-2452

X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.
Laskowski RA, Thornton JM, Humblet C, Singh J.
J Mol Biol Volume 259 (1996) p.175-201
DOI: 10.1006/jmbi.1996.0311

Protein fold recognition by sequence threading: tools and assessment techniques.
Miller RT, Jones DT, Thornton JM.
FASEB J Volume 10 (1996) p.171-178

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.
Viles JH, Mitchell JB, Gough SL, Doyle PM, Harris CJ, Sadler PJ, Thornton JM.
Eur J Biochem Volume 242 (1996) p.352-362
DOI: 10.1111/j.1432-1033.1996.0352r.x

Molecular recognition by proteins: protein-ligand interactions from a structural perspective.
Wallace AC, Laskowski RA, Singh J, Thornton JM.
Biochem Soc Trans Volume 24 (1996) p.280-284

Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM.
J Mol Biol Volume 255 (1996) p.494-506
DOI: 10.1006/jmbi.1996.0041

PROMOTIF--a program to identify and analyze structural motifs in proteins.
Hutchinson EG, Thornton JM.
Protein Sci Volume 5 (1996) p.212-220
DOI: 10.1002/pro.5560050204

Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.
Kalsi JK, Martin AC, Hirabayashi Y, Ehrenstein M, Longhurst CM, Ravirajan C, Zvelebil M, Stollar BD, Thornton JM, Isenberg DA.
Mol Immunol Volume 33 (1996) p.471-483
DOI: 10.1016/0161-5890(95)00138-7

Principles of protein-protein interactions.
Jones S, Thornton JM.
Proc Natl Acad Sci U S A Volume 93 (1996) p.13-20
DOI: 10.1073/pnas.93.1.13

Protein recognition of adenylate: an example of a fuzzy recognition template.
Moodie SL, Mitchell JB, Thornton JM.
J Mol Biol Volume 263 (1996) p.486-500
DOI: 10.1006/jmbi.1996.0591

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.
Martin AC, Thornton JM.
J Mol Biol Volume 263 (1996) p.800-815
DOI: 10.1006/jmbi.1996.0617

Potential energy functions for threading.
Jones DT, Thornton JM.
Curr Opin Struct Biol Volume 6 (1996) p.210-216
DOI: 10.1016/s0959-440x(96)80076-5

Antibody-antigen interactions: contact analysis and binding site topography.
MacCallum RM, Martin AC, Thornton JM.
J Mol Biol Volume 262 (1996) p.732-745
DOI: 10.1006/jmbi.1996.0548

Analysis of domain structural class using an automated class assignment protocol.
Michie AD, Orengo CA, Thornton JM.
J Mol Biol Volume 262 (1996) p.168-185
DOI: 10.1006/jmbi.1996.0506

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM.
J Biomol NMR Volume 8 (1996) p.477-486
DOI: 10.1007/bf00228148

Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic.
Doyle PM, Harris JC, Moody CM, Sadler PJ, Sims M, Thornton JM, Uppenbrink J, Viles JH.
Int J Pept Protein Res Volume 47 (1996) p.427-436

Chirality in Protein Structure
Slidel TWF, Thornton JM.
Volume (1996) p.253-264

Deviations from planarity of the peptide bond in peptides and proteins.
MacArthur MW, Thornton JM.
J Mol Biol Volume 264 (1996) p.1180-1195
DOI: 10.1006/jmbi.1996.0705

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.
Wallace AC, Laskowski RA, Thornton JM.
Protein Sci Volume 5 (1996) p.1001-1013
DOI: 10.1002/pro.5560050603

Towards meeting the Paracelsus Challenge: The design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50% sequence identity to an all-beta protein.
Jones DT, Moody CM, Uppenbrink J, Viles JH, Doyle PM, Harris CJ, Pearl LH, Sadler PJ, Thornton JM.
Proteins Volume 24 (1996) p.502-513
DOI: 10.1002/(sici)1097-0134(199604)24:4<502::aid-prot9>3.0.co;2-f

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.
Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J.
Trends Biochem Sci Volume 21 (1996) p.251-256
DOI: 10.1016/0968-0004(96)10037-2

1995

Modelling the Interaction of Protein Side Chains
Mitchell JBO, Thornton JM, Price SL.
Volume (1995) p.119-135

Protein folds: towards understanding folding from inspection of native structures.
Thornton JM, Jones DT, MacArthur MW, Orengo CM, Swindells MB.
Philos Trans R Soc Lond B Biol Sci Volume 348 (1995) p.71-79
DOI: 10.1098/rstb.1995.0047

The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains.
McDonald IK, Thornton JM.
Protein Eng Volume 8 (1995) p.217-224
DOI: 10.1093/protein/8.3.217

Folding of Beta Structure in Proteins
Evans PA, Gladwin ST, Gopalakrishnan B, Tisi LC, Woolfson DN, Murracy JH, Packman LC, Trotter BW, Mackay JP, Williams DH, Thornton JM.
FASEB J Volume 9 (1995) p.a1239

Protein Engineering - Editorial Overview
Thornton JM, Berg JM.
Volume (1995) p.367-369

Protein Folds and Folding
Thornton JM, Jones DT, MacArthur M, Orengo CA, Swindells M.
FASEB J Volume 9 (1995) p.a1240

Protein-protein interactions: a review of protein dimer structures.
Jones S, Thornton JM.
Prog Biophys Mol Biol Volume 63 (1995) p.31-65
DOI: 10.1016/0079-6107(94)00008-w

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.
Swindells MB, MacArthur MW, Thornton JM.
Nat Struct Biol Volume 2 (1995) p.596-603
DOI: 10.1038/nsb0795-596

Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity.
Orengo CA, Swindells MB, Michie AD, Zvelebil MJ, Driscoll PC, Waterfield MD, Thornton JM.
Protein Sci Volume 4 (1995) p.1977-1983
DOI: 10.1002/pro.5560041003

Chirality in Proteins
Slidel TMW, Thornton JM.
Volume (1995) p.253-264

Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Jones DT, Miller RT, Thornton JM.
Proteins Volume 23 (1995) p.387-397
DOI: 10.1002/prot.340230312

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Wallace AC, Laskowski RA, Thornton JM.
Protein Eng Volume 8 (1995) p.127-134
DOI: 10.1093/protein/8.2.127

Long loops in proteins.
Martin AC, Toda K, Stirk HJ, Thornton JM.
Protein Eng Volume 8 (1995) p.1093-1101
DOI: 10.1093/protein/8.11.1093

1994

Knowledge-based validation of protein-structure coordinates derived by x-ray Cyrstallography and NMR-Spectroscopy
MacArthur MW, Laskowski RA, Thornton JM.
Volume (1994) p.731-737

A model recognition approach to the prediction of all-helical membrane protein structure and topology.
Jones DT, Taylor WR, Thornton JM.
Biochemistry Volume 33 (1994) p.3038-3049
DOI: 10.1021/bi00176a037

Protein Motifs and Folding Recognition
Thornton JM, Orengo CM, Jones DT, Taylor WR.
Biophys J Volume 66 (1994) p.a241

Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
Mitchell JB, Nandi CL, McDonald IK, Thornton JM, Price SL.
J Mol Biol Volume 239 (1994) p.315-331
DOI: 10.1006/jmbi.1994.1370

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Hubbard SJ, Eisenmenger F, Thornton JM.
Protein Sci Volume 3 (1994) p.757-768
DOI: 10.1002/pro.5560030505

Protein superfamilies and domain superfolds.
Orengo CA, Jones DT, Thornton JM.
Nature Volume 372 (1994) p.631-634
DOI: 10.1038/372631a0

A mutation data matrix for transmembrane proteins.
Jones DT, Taylor WR, Thornton JM.
FEBS Lett Volume 339 (1994) p.269-275
DOI: 10.1016/0014-5793(94)80429-x

A revised set of potentials for beta-turn formation in proteins.
Hutchinson EG, Thornton JM.
Protein Sci Volume 3 (1994) p.2207-2216
DOI: 10.1002/pro.5560031206

Satisfying hydrogen bonding potential in proteins.
McDonald IK, Thornton JM.
J Mol Biol Volume 238 (1994) p.777-793
DOI: 10.1006/jmbi.1994.1334

An algorithm for automatically generating protein topology cartoons.
Flores TP, Moss DS, Thornton JM.
Protein Eng Volume 7 (1994) p.31-37
DOI: 10.1093/protein/7.1.31

Buried waters and internal cavities in monomeric proteins.
Williams MA, Goodfellow JM, Thornton JM.
Protein Sci Volume 3 (1994) p.1224-1235
DOI: 10.1002/pro.5560030808

The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.
Stirk HJ, Thornton JM.
Protein Eng Volume 7 (1994) p.47-56
DOI: 10.1093/protein/7.1.47

NMR and crystallography--complementary approaches to structure determination.
MacArthur MW, Driscoll PC, Thornton JM.
Trends Biotechnol Volume 12 (1994) p.149-153
DOI: 10.1016/0167-7799(94)90074-4

Evaluation of Protein Coordinate Data Sets
Laskowski RA, MacArthur MW, Thornton JM.
Volume (1994) p.149-159

1993

A study of structural determinants in the interleukin-1 fold.
Swindells MB, Thornton JM.
Protein Eng Volume 6 (1993) p.711-715
DOI: 10.1093/protein/6.7.711

Recurring structural motifs in proteins with different functions.
Orengo CA, Flores TP, Jones DT, Taylor WR, Thornton JM.
Curr Biol Volume 3 (1993) p.131-139
DOI: 10.1016/0960-9822(93)90254-l

Molecular modelling and epitope prediction of gp29 from lymphatic filariae.
Zvelebil MJ, Tang L, Cookson E, Selkirk ME, Thornton JM.
Mol Biochem Parasitol Volume 58 (1993) p.145-153
DOI: 10.1016/0166-6851(93)90098-i

Peptide-protein interactions: an overview.
Zvelebil MJ, Thornton JM.
Q Rev Biophys Volume 26 (1993) p.333-363
DOI: 10.1017/s0033583500002870

PROCHECK: a program to check the stereochemical quality of protein structures.
Laskowski RA, MacArthur MW, Moss DS, Thornton JM.
J Appl Crystallogr Volume 26 (1993) p.283-291
DOI: 10.1107/s0021889892009944

Chain Topologies Copmatible with a Antiparallel Six-Stranded b-sandwich: Predominance of Greek Key Protein Structures
Wooflson DN, Evans PA, Hutchinson EG, Thornton JM.
Protein Sci Volume 6 (1993) p.461-470

Main-chain bond lengths and bond angles in protein structures.
Laskowski RA, Moss DS, Thornton JM.
J Mol Biol Volume 231 (1993) p.1049-1067
DOI: 10.1006/jmbi.1993.1351

Comparison of conformational characteristics in structurally similar protein pairs.
Flores TP, Orengo CA, Moss DS, Thornton JM.
Protein Sci Volume 2 (1993) p.1811-1826
DOI: 10.1002/pro.5560021104

Identification, classification, and analysis of beta-bulges in proteins.
Chan AW, Hutchinson EG, Harris D, Thornton JM.
Protein Sci Volume 2 (1993) p.1574-1590
DOI: 10.1002/pro.5560021004

Accommodating sequence changes in beta-hairpins in proteins.
Sibanda BL, Thornton JM.
J Mol Biol Volume 229 (1993) p.428-447
DOI: 10.1006/jmbi.1993.1044

Structures of Antifungal Thionin Proteins - H-1-NMR of SI-Alpha-1 from Sorghum Seeds
Bloch C, Patel SU, Sadler PJ, Zvelebil M, Thornton JM.
J Cell Biochem Volume (1993) p.270

Shared Structural Motif in Proteins - Reply
Swindells MJ, Orengo CA, Jones DT, Pearl LH, Thornton JM.
Nature Volume 365 (1993) p.21

Protein Structures and Complexes - What they reveal about the interactions that stabilize them
Thornton JM, MacArthur MW, McDonald IK, Jones DT, Mitchell JBO, Nandi CL, Price SL, Zvelebil M.
Volume (1993) p.113-129

Modelling of related protein structures
Thornton JM, Swindells MB.
Volume (1993) p.82-113

Database Analysis for Protein Engineering
Thornton JM, Gardner SP.
Volume (1993) p.18-22

A Compairson to Three Theoretical Approaches to the Study of Side-Chain Interactions in Proteins
Mitchell JBO, Nandi CL, Price SL, Singh J, Snarey M, Thornton JM.
Journal of the Chemical Society. Faraday Trans Volume 89 (1993) p.2619-2630

The Cuticular Peroxidase of Filarial Parasites - a Potential Target for Drug Design
Selkirk ME, Zvelebil M, Tang L, Cookson E, Thornton JM.
J Cell Biochem Volume (1993) p.226

Progress Towards Recognizing Protein Folds from Amino-Acid-Sequence
Jones DT, Orengo C, Taylor WR, Thornton JM.
Protein Eng Volume 6 (1993) p.124

Amino Aromatic Interactions
Mitchell JBO, Nandi CL, Ali S, McDonald JK, Thornton JM, Price SL, Singh J.
Nature Volume 366 (1993) p.413

A study into the effects of protein binding on nucleotide conformation.
Moodie SL, Thornton JM.
Nucleic Acids Res Volume 21 (1993) p.1369-1380
DOI: 10.1093/nar/21.6.1369

Recurrence of a binding motif?
Swindells MB, Orengo CA, Jones DT, Pearl LH, Thornton JM.
Nature Volume 362 (1993) p.299
DOI: 10.1038/362299a0

Conformational analysis of protein structures derived from NMR data.
MacArthur MW, Thornton JM.
Proteins Volume 17 (1993) p.232-251
DOI: 10.1002/prot.340170303

Atomic environments of arginine side chains in proteins.
Nandi CL, Singh J, Thornton JM.
Protein Eng Volume 6 (1993) p.247-259
DOI: 10.1093/protein/6.3.247

The Greek key motif: extraction, classification and analysis.
Hutchinson EG, Thornton JM.
Protein Eng Volume 6 (1993) p.233-245
DOI: 10.1093/protein/6.3.233

Alpha plus beta folds revisited: some favoured motifs.
Orengo CA, Thornton JM.
Structure Volume 1 (1993) p.105-120
DOI: 10.1016/0969-2126(93)90026-d

Protein fold recognition.
Jones D, Thornton J.
J Comput Aided Mol Des Volume 7 (1993) p.439-456
DOI: 10.1007/bf02337560

Identification and classification of protein fold families.
Orengo CA, Flores TP, Taylor WR, Thornton JM.
Protein Eng Volume 6 (1993) p.485-500
DOI: 10.1093/protein/6.5.485

Topological and stereochemical restrictions in beta-sandwich protein structures.
Woolfson DN, Evans PA, Hutchinson EG, Thornton JM.
Protein Eng Volume 6 (1993) p.461-470
DOI: 10.1093/protein/6.5.461

1992

Protein Structures: The End Point of the Folding Pathway
Thornton JM.
Volume (1992) p.63-86

Depicting topology and handedness in jellyroll structures.
Stirk HJ, Woolfson DN, Hutchinson EG, Thornton JM.
FEBS Lett Volume 308 (1992) p.1-3
DOI: 10.1016/0014-5793(92)81036-l

Stereochemical quality of protein structure coordinates.
Morris AL, MacArthur MW, Hutchinson EG, Thornton JM.
Proteins Volume 12 (1992) p.345-364
DOI: 10.1002/prot.340120407

The rapid generation of mutation data matrices from protein sequences.
Jones DT, Taylor WR, Thornton JM.
Comput Appl Biosci Volume 8 (1992) p.275-282

Substrate recognition by proteinases.
Hubbard SJ, Thornton JM, Campbell SF.
Faraday Discuss Volume (1992) p.13-23

Towards an understanding how side-chains pack in proteins
Singh J, Nandi LC, Thornton JM.
Volume (1992) p.1-18

Lessons in Analysing Protein Structures
Thornton JM.
Volume (1992) p.888-894

A new approach to protein fold recognition.
Jones DT, Taylor WR, Thornton JM.
Nature Volume 358 (1992) p.86-89
DOI: 10.1038/358086a0

Secondary and Supersecondary Motifs in Protein Structures
Thornton JM, Sibanda BL, Wilmott CM, Singh J.
Volume (1992) p.141-156

Atlas of Protein Side-Chain Interactions
Singh J, Thornton JM.
Volume (1992) p.

A topological model for hepatitis B surface antigen.
Stirk HJ, Thornton JM, Howard CR.
Intervirology Volume 33 (1992) p.148-158

Towards an understanding of the arginine-aspartate interaction.
Mitchell JB, Thornton JM, Singh J, Price SL.
J Mol Biol Volume 226 (1992) p.251-262
DOI: 10.1016/0022-2836(92)90137-9

1991

Modelling antibody combining sites: a review.
Thornton JM.
Ciba Found Symp Volume 159 (1991) p.55-69; discussion 69-71

Protein structure. Prediction of progress at last.
Thornton JM, Flores TP, Jones DT, Swindells MB.
Nature Volume 354 (1991) p.105-106
DOI: 10.1038/354105a0

Protein Structure Database
Thornton JM, Gardner SP, Hutchinson EG.
Volume (1991) p.

Conformation of beta hairpins in protein structures: classification and diversity in homologous structures.
Sibanda BL, Thornton JM.
Methods Enzymol Volume 202 (1991) p.59-82
DOI: 10.1016/0076-6879(91)02007-v

Trypanothine Metabolism as a Target for Drug Design: Molecular Modelling of Trypanothine Reductase in Biochemical Protozoology
Smith K, Mills A, Thornton JM, Fairlamb AH.
Volume (1991) p.482-492

Structural Patterns in Globular Proteins
Hutchinson EG, Morris AL, Thornton JM.
Volume (1991) p.

Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins.
Hunter CA, Singh J, Thornton JM.
J Mol Biol Volume 218 (1991) p.837-846
DOI: 10.1016/0022-2836(91)90271-7

A novel method for the modelling of peptide ligands to their receptors.
Singh J, Saldanha J, Thornton JM.
Protein Eng Volume 4 (1991) p.251-261
DOI: 10.1093/protein/4.3.251

Protein Structure
Thornton JM, Barlow DJ.
Volume (1991) p.9-30

Structure prediction and modelling.
Swindells MB, Thornton JM.
Curr Opin Biotechnol Volume 2 (1991) p.512-519
DOI: 10.1016/0958-1669(91)90074-f

Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors.
Hubbard SJ, Campbell SF, Thornton JM.
J Mol Biol Volume 220 (1991) p.507-530
DOI: 10.1016/0022-2836(91)90027-4

The Iditis Relational Database of Protein Structure
Gardner SP, Thornton JM.
Volume (1991) p.32

Protein Structure, Prediction and Design
Thornton JM.
Volume (1991) p.

Modelling by Homology
Swindells MB, Thornton JM.
Volume (1991) p.219-223

Influence of proline residues on protein conformation.
MacArthur MW, Thornton JM.
J Mol Biol Volume 218 (1991) p.397-412
DOI: 10.1016/0022-2836(91)90721-h

Analysis of protein main-chain solvation as a function of secondary structure.
Thanki N, Umrania Y, Thornton JM, Goodfellow JM.
J Mol Biol Volume 221 (1991) p.669-691
DOI: 10.1016/0022-2836(91)80080-e

An extension of secondary structure prediction towards the prediction of tertiary structure.
Garratt RC, Thornton JM, Taylor WR.
FEBS Lett Volume 280 (1991) p.141-146
DOI: 10.1016/0014-5793(91)80223-p

1990

Antibody Modelling - Tackling a Loopy Problem
Thornton JM.
Nature Volume 343 (1990) p.411-412
DOI: pmid: 2300188

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups.
Singh J, Thornton JM.
J Mol Biol Volume 211 (1990) p.595-615
DOI: 10.1016/0022-2836(90)90268-q

Beta-turns and their distortions: a proposed new nomenclature.
Wilmot CM, Thornton JM.
Protein Eng Volume 3 (1990) p.479-493
DOI: 10.1093/protein/3.6.479

Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins.
Thanki N, Thornton JM, Goodfellow JM.
Protein Eng Volume 3 (1990) p.495-508
DOI: 10.1093/protein/3.6.495

HERA--a program to draw schematic diagrams of protein secondary structures.
Hutchinson EG, Thornton JM.
Proteins Volume 8 (1990) p.203-212
DOI: 10.1002/prot.340080303

1989

Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.
Rooman MJ, Wodak SJ, Thornton JM.
Protein Eng Volume 3 (1989) p.23-27
DOI: 10.1093/protein/3.1.23

Protein Engineering and Design
Blundell TL, Elliott G, Gardner SP, Hubbard T, Islam S, Johnson M, Mantafounis D, Sutcliffe MJ, Thornton JM, Travers P.
Philos Trans R Soc Lond B Biol Sci Volume 324 (1989) p.447-460

Rebuilding flavodoxin from C alpha coordinates: a test study.
Reid LS, Thornton JM.
Proteins Volume 5 (1989) p.170-182
DOI: 10.1002/prot.340050212

Preliminary Analysis of Water Molecule Disitributions in Proteins
Goodfellow JM, Thanki N, Thornton JM.
Mol Simul Volume 3 (1989) p.167-182

Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.
Sibanda BL, Blundell TL, Thornton JM.
J Mol Biol Volume 206 (1989) p.759-777
DOI: 10.1016/0022-2836(89)90583-4

Structure Prediction
Thornton JM, Taylor WR.
Volume (1989) p.147-190

Protein motifs and data-base searching.
Thornton JM, Gardner SP.
Trends Biochem Sci Volume 14 (1989) p.300-304
DOI: 10.1016/0968-0004(89)90069-8

1988

Specialist Periodical Report
Thornton JM, Singh J, Campbell S, Bludell TL.
Volume (1988) p.189-198

Protein-protein recognition via side-chain interactions.
Thornton JM, Singh J, Campbell S, Blundell TL.
Biochem Soc Trans Volume 16 (1988) p.927-930

An Integrated Sequence and Structure Database
Akrigg D, Bleasby AJ, Dix NIM, Findley JBC, North ACT, Parry-Smith W, Tickle IJ, Murray-Rust P.
Nature Volume 335 (1988) p.745-746

Analysis and prediction of the different types of beta-turn in proteins.
Wilmot CM, Thornton JM.
J Mol Biol Volume 203 (1988) p.221-232
DOI: 10.1016/0022-2836(88)90103-9

Distributions of water around amino acid residues in proteins.
Thanki N, Thornton JM, Goodfellow JM.
J Mol Biol Volume 202 (1988) p.637-657
DOI: 10.1016/0022-2836(88)90292-6

Protein structure. The shape of things to come?
Thornton JM.
Nature Volume 335 (1988) p.10-11
DOI: 10.1038/335010a0

Analysis, design and modification of loop regions in proteins.
Thornton JM, Sibanda BL, Edwards MS, Barlow DJ.
Bioessays Volume 8 (1988) p.63-69
DOI: 10.1002/bies.950080205

Helix geometry in proteins.
Barlow DJ, Thornton JM.
J Mol Biol Volume 201 (1988) p.601-619
DOI: 10.1016/0022-2836(88)90641-9

1987

Prediction of Protein Tertiary Structure from C-Alpha Atomic Coordinates
Reid LS, Thornton JM, Blundell T.
J Cell Biochem Volume (1987) p.230

Prediction of Protein Structure from C-Alpha Atomic Coordinates
Reid LS, Thornton JM.
Volume (1987) p.

Knowledge-based prediction of protein structures and the design of novel molecules.
Blundell TL, Sibanda BL, Sternberg MJ, Thornton JM.
Nature Volume 326 (1987) p.347-352
DOI: 10.1038/326347a0

Structural and sequence patterns in the loops of beta alpha beta units.
Edwards MS, Sternberg JE, Thornton JM.
Protein Eng Volume 1 (1987) p.173-181
DOI: 10.1093/protein/1.3.173

Protein Structure Analysis - A Basis for Structure Prediction
Thornton JM, Barlow DJ, Edwards MS, Sibanda BL, Singh J, Wilmot CM.
Volume (1987) p.1-22

Protein Engineering '87 Conference Report
Wetzel R, Thornton JM, Gait M.
Protein Eng Volume 1 (1987) p.267-274

The geometries of interacting arginine-carboxyls in proteins.
Singh J, Thornton JM, Snarey M, Campbell SF.
FEBS Lett Volume 224 (1987) p.161-171
DOI: 10.1016/0014-5793(87)80441-6

Structure, Design and Modification of Loop Regions in Proteins
Thornton JM, Sibanda BL, Edwards MJ, Barlow DJ.
Protein Eng Volume 1 (1987) p.227

Structural Survey (Review of Introduction to Proteins and Protein Engineering)
Thornton JM.
Nature Volume 328 (1987) p.584
DOI: 10.1038/328584a0

Protein Engineering
Thornton JM.
Nature Volume 330 (1987) p.430

Building and Design
Thornton JM.
Nature Volume 330 (1987) p.430

1986

Aromatic Interactions
Blundell TL, Singh J, Thornton JM, Burley SK, Petsko GA.
Science (80- ) Volume 234 (1986) p.1005
DOI: 10.1126/science.3775369

The Non-Random Loop Regions In Proteins
Thornton JM.
Fed Proc Volume 45 (1986) p.1829

Application of Computer Graphics in the Study of Drug-Receptor Interactions
Thornton JM, Barlow DJ, Sternberg MJE.
Volume (1986) p.102-118

The distribution of charged groups in proteins.
Barlow DJ, Thornton JM.
Biopolymers Volume 25 (1986) p.1717-1733
DOI: 10.1002/bip.360250913

Continuous and discontinuous protein antigenic determinants.
Barlow DJ, Edwards MS, Thornton JM.
Nature Volume 322 (1986) p.747-748
DOI: 10.1038/322747a0

Location of 'continuous' antigenic determinants in the protruding regions of proteins.
Thornton JM, Edwards MS, Taylor WR, Barlow DJ.
EMBO J Volume 5 (1986) p.409-413

Interactive Map Projection
Barlow DJ, Thornton JM.
J Mol Graph Volume 4 (1986) p.97

1985

Sulfur-Aromatic Interactions in Proteins
Reid KSC, Lindley PF, Thornton JM.
FEBS Lett Volume 190 (1985) p.209-213

Variability, Modelling and Prediction of Beta-Hairpins with reference to the immunoglobulin fold
Thornton JM, Sibanda BL, Taylor WR.
Volume (1985) p.23-32

The Influence of Tertiary Structure on Secondary Structure Prediction - Accessiblity Versus Predictability for Beta-Structure
Garratt RC, Taylor WR, Thornton JM.
FEBS Lett Volume 188 (1985) p.59-62

Beta-hairpin families in globular proteins.
Sibanda BL, Thornton JM.
Nature Volume 316 (1985) p.170-174
DOI: 10.1038/316170a0

A Novel-Approach for Identifying Potential Antigenic Determinants from the 3d Structure of a Protein
Thornton JM, Edwards MS, Taylor WR, Barlow DJ.
J Mol Graph Volume 3 (1985) p.105-106

The Interactoin Between Phenylalanine Rings in Proteins
Singh J, Thornton JM.
FEBS Lett Volume 191 (1985) p.1-6

1984

Recognition of super-secondary structure in proteins.
Taylor WR, Thornton JM.
J Mol Biol Volume 173 (1984) p.487-512
DOI: 10.1016/0022-2836(84)90393-0

1983

Prediction of super-secondary structure in proteins.
Taylor WR, Thornton JM.
Nature Volume 301 (1983) p.540-542
DOI: 10.1038/301540a0

Ion-pairs in proteins.
Barlow DJ, Thornton JM.
J Mol Biol Volume 168 (1983) p.867-885
DOI: 10.1016/s0022-2836(83)80079-5

Solvent-induced distortions and the curvature of alpha-helices.
Blundell T, Barlow D, Borkakoti N, Thornton J.
Nature Volume 306 (1983) p.281-283
DOI: 10.1038/306281a0

Amino and carboxy-terminal regions in globular proteins.
Thornton JM, Sibanda BL.
J Mol Biol Volume 167 (1983) p.443-460
DOI: 10.1016/s0022-2836(83)80344-1

An Ellipsoidal Approximation to Protein Shape
Taylor WR, Thornton JM, Turnell WG.
J Mol Graph Volume 1 (1983) p.30-38

1982

Electrostatic interactions in proteins.
Thornton JM.
Nature Volume 295 (1982) p.13-14
DOI: 10.1038/295013a0

Conformation of terminal regions in proteins.
Thornton JM, Chakauya BL.
Nature Volume 298 (1982) p.296-297
DOI: 10.1038/298296a0

1981

Disulphide bridges in globular proteins.
Thornton JM.
J Mol Biol Volume 151 (1981) p.261-287
DOI: 10.1016/0022-2836(81)90515-5

1978

An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase.
Phillips DC, Sternberg MJ, Thornton JM, Wilson IA.
J Mol Biol Volume 119 (1978) p.329-351
DOI: 10.1016/0022-2836(78)90440-0

Prediction of protein structure from amino acid sequence.
Sternberg MJ, Thornton JM.
Nature Volume 271 (1978) p.15-20
DOI: 10.1038/271015a0

Comparison of the calcium- and magnesium-induced structural changes of troponin--C. A proton magnetic resonance study.
Levine BA, Thornton JM, Fernandes R, Kelly CM, Mercola D.
Biochim Biophys Acta Volume 535 (1978) p.11-24
DOI: 10.1016/0005-2795(78)90028-4

Prediction of protein structure from amino acid sequence.
Sternberg MJ, Thornton JM.
Biochem Soc Trans Volume 6 (1978) p.1119-1123

1977

An analysis of the three-dimensional structure of chicken triose phosphate isomerase.
Phillips DC, Rivers PS, Sternberg MJ, Thornton JM, Wilson IA.
Biochem Soc Trans Volume 5 (1977) p.642-647

On the conformation of proteins: the handedness of the connection between parallel beta-strands.
Sternberg MJ, Thornton JM.
J Mol Biol Volume 110 (1977) p.269-283
DOI: 10.1016/s0022-2836(77)80072-7

On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets.
Sternberg MJ, Thornton JM.
J Mol Biol Volume 115 (1977) p.1-17
DOI: 10.1016/0022-2836(77)90242-x

On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets.
Sternberg MJ, Thornton JM.
J Mol Biol Volume 113 (1977) p.401-418
DOI: 10.1016/0022-2836(77)90149-8

Calcium binding by troponin-C. A proton magnetic resonance study.
Levine BA, Coffman DM, Thornton JM.
J Mol Biol Volume 115 (1977) p.743-760
DOI: 10.1016/0022-2836(77)90113-9

On the conformation of proteins: an analysis of beta-pleated sheets.
Sternberg MJ, Thornton JM.
J Mol Biol Volume 110 (1977) p.285-296
DOI: 10.1016/s0022-2836(77)80073-9

Conformational energy calculations for dinucleotide molecules: a study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+).
Thornton JM, Bayley PM.
Biopolymers Volume 16 (1977) p.1971-1986
DOI: 10.1002/bip.1977.360160911

1976

Proton magnetic resonance study of troponin-C.
Levine BA, Mercola D, Thornton JM.
FEBS Lett Volume 61 (1976) p.218-222
DOI: 10.1016/0014-5793(76)81041-1

Computer techniques for conformational studies of biological molecules.
Perkins WJ, Piper EA, Thornton J.
Comput Biol Med Volume 6 (1976) p.23-31
DOI: 10.1016/0010-4825(76)90034-2

Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate.
Thornton JM, Bayley PM.
Biopolymers Volume 15 (1976) p.955-975
DOI: 10.1002/bip.1976.360150511

On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit.
Sternberg MJ, Thornton JM.
J Mol Biol Volume 105 (1976) p.367-382
DOI: 10.1016/0022-2836(76)90099-1

1975

Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magnetic-resonance probes.
Tanswell P, Thornton JM, Korda AV, Williams RJ.
Eur J Biochem Volume 57 (1975) p.135-145
DOI: 10.1111/j.1432-1033.1975.tb02284.x

Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate.
Thornton JM, Bayley PM.
Biochem J Volume 149 (1975) p.585-596

A nuclear magnetic resonance investigation of the conformation of nicotinamide mononucleotide in aqueous solution.
Birdsall B, Birdsall NJ, Feeney J, Thornton J.
J Am Chem Soc Volume 97 (1975) p.2845-2850
DOI: 10.1021/ja00843a039

0

Handbook of Cell Signalling
Nooren MA, Thornton JM.
Volume (0) p.

Protein Structure Classification
Pearl FMG, Orengo CA, Thornton JM.
Volume (0) p.

Services

Team members

Marco Brandizi
Jon Chambers
Nathalie Conte
Tom Hancocks
Ingvar Lagerstedt
Olga Melnichuk
Tina Perica