Publications

2014

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 (2014) p.

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

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

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

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

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

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

Gene cooption in mycobacteria and search for virulence attributes: comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other mycobacteria.
Singh Y, Kohli S, Sowpati DT, Rahman SA, Tyagi AK, Hasnain SE.
Int J Med Microbiol Volume 304 (2014) p.742-748

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

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

2013

Mucosal addressin cell adhesion molecule (MAdCAM-1) expression is upregulated in the cirrhotic liver and immunolocalises to the peribiliary plexus and lymphoid aggregates.
Ala A, Brown D, Khan K, Standish R, Odin JA, Fiel MI, Schiano TD, Hillan KJ, Rahman SA, Hodgson HJ, Dhillon AP.
Dig Dis Sci Volume 58 (2013) p.2528-2541

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

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

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

A genome-wide study shows a limited contribution of rare copy number variants to Alzheimer's disease risk.
Chapman J, Rees E, Harold D, Ivanov D, Gerrish A, Sims R, Hollingworth P, Stretton A, GERAD1 Consortium, Holmans P, Owen MJ, O'Donovan MC, Williams J, Kirov G.
Hum Mol Genet Volume 22 (2013) p.816-824

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

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

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

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

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

The Ramachandran plot and protein structure validation
Laskowski RA, Furnham N, Thornton JM.
Volume (2013) p.62-75

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

Implication of a rare deletion at distal 16p11.2 in schizophrenia.
Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, Malhotra AK, Rietschel M, Nöthen MM, Degenhardt F, Priebe L, Breuer R, Strohmaier J, Ruderfer DM, Moran JL, Chambert KD, Sanders AR, Shi J, Kendler K, Riley B, O'Neill T, Walsh D, Malhotra D, Corvin A, Purcell S, Sklar P, Iwata N, Hultman CM, Sullivan PF, Sebat J, McCarthy S, Gejman PV, Levinson DF, Owen MJ, O'Donovan MC, Lencz T, Kirov G, Molecular Genetics of Schizophrenia Consortium, Wellcome Trust Case Control Consortium 2.
JAMA Psychiatry Volume 70 (2013) p.253-260

Serotonin: from top to bottom.
Fidalgo S, Ivanov DK, Wood SH.
Biogerontology Volume 14 (2013) p.21-45

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

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

Women in science.
Dean C, Osborn M, Oshlack A, Thornton J.
Genome Biol Volume 13 (2012) p.148

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

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

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

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

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

Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles.
Wang T, Schiffels D, Cuesta SM, Fygenson DK, Seeman NC.
J Am Chem Soc Volume 134 (2012) p.1606-1616

De novo induction of amyloid-β deposition in vivo.
Morales R, Duran-Aniotz C, Castilla J, Estrada LD, Soto C.
Mol Psychiatry Volume 17 (2012) p.1347-1353

MACiE: exploring the diversity of biochemical reactions.
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.
Nucleic Acids Res Volume 40 (2012) p.d783-9

De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.
Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M, Ruderfer D, Moran J, Chambert K, Toncheva D, Georgieva L, Grozeva D, Fjodorova M, Wollerton R, Rees E, Nikolov I, van de Lagemaat LN, Bayés A, Fernandez E, Olason PI, Böttcher Y, Komiyama NH, Collins MO, Choudhary J, Stefansson K, Stefansson H, Grant SG, Purcell S, Sklar P, O'Donovan MC, Owen MJ.
Mol Psychiatry Volume 17 (2012) p.142-153

2011

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

Protein structure databases.
Laskowski RA.
Mol Biotechnol Volume 48 (2011) p.183-198

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

Celebrating structural biology.

Nat Struct Mol Biol Volume 18 (2011) p.1304-1316

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

Structural annotation of Mycobacterium tuberculosis proteome.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R, OSDD Consortium, Brahmachari SK, Chandra N.
PLoS One Volume 6 (2011) p.e27044

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
J Chem Inf Model Volume 51 (2011) p.2778-2786

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

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

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

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

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.
Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP.
Genome Biol Volume 12 (2011) p.r90

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

2010

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

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

Domain-ligand mapping for enzymes.
Bashton M, Thornton JM.
J Mol Recognit Volume 23 (2010) p.194-208

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

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

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

Protein structure databases.
Laskowski RA.
Methods Mol Biol Volume 609 (2010) p.59-82

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan AW, Laskowski RA, Selwood DL.
J Med Chem Volume 53 (2010) p.3086-3094

Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.
Nat Methods Volume 7 (2010) p.s42-55

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri AU, Laskowski RA.
Bioinformatics Volume 26 (2010) p.1260-1261

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

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

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

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

2009

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

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

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

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

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

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

PDBsum new things.
Laskowski RA.
Nucleic Acids Res Volume 37 (2009) p.d355-9

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

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

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

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

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

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

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

The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM.
FEBS Lett Volume 583 (2009) p.1692-1698

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

Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.
J Cheminform Volume 1 (2009) p.12

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

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

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

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

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

Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network.
Genome Biol Volume 10 (2009) p.401

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

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJ, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AF, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C.
Nat Genet Volume 41 (2009) p.1182-1190

Integrated Servers for Structure-Informed Function Prediction
Laskowski RA.
Volume (2009) p.251-272

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

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

2008

Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM.
BMC Evol Biol Volume 8 (2008) p.247

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

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

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

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

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

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

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

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

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

2007

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

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

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

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

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

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

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

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

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

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

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

The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.
J Mol Biol Volume 372 (2007) p.1261-1277

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

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA.
Bioinformatics Volume 23 (2007) p.1824-1827

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

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

2006

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.
Devi SM, Ahmed I, Khan AA, Rahman SA, Alvi A, Sechi LA, Ahmed N.
BMC Genomics Volume 7 (2006) p.191

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

Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
J Mol Biol Volume 364 (2006) p.836-852

Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks.
Rahman SA, Schomburg D.
Bioinformatics Volume 22 (2006) p.1767-1774

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

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

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

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

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

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

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM.
J Mol Biol Volume 356 (2006) p.928-944

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

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

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

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

2005

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

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

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

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

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

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

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

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

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

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

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

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

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

Conformational changes observed in enzyme crystal structures upon substrate binding.
Gutteridge A, Thornton J.
J Mol Biol Volume 346 (2005) p.21-28

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

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

Understanding nature's catalytic toolkit.
Gutteridge A, Thornton JM.
Trends Biochem Sci Volume 30 (2005) p.622-629

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

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

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

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

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

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

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

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

Protein families and their evolution-a structural perspective.
Orengo CA, Thornton JM.
Annu Rev Biochem Volume 74 (2005) p.867-900

2004

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

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

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

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

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

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

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

Searching for functional sites in protein structures.
Jones S, Thornton JM.
Curr Opin Chem Biol Volume 8 (2004) p.3-7

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

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

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

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

X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.
Savchenko A, Skarina T, Evdokimova E, Watson JD, Laskowski R, Arrowsmith CH, Edwards AM, Joachimiak A, Zhang RG.
Proteins Volume 54 (2004) p.162-165

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

2003

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

Diversity of protein-protein interactions.
Nooren IM, Thornton JM.
EMBO J Volume 22 (2003) p.3486-3492

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

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

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

Molecular basis of inherited diseases: a structural perspective.
Steward RE, MacArthur MW, Laskowski RA, Thornton JM.
Trends Genet Volume 19 (2003) p.505-513

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

Structural characterisation and functional significance of transient protein-protein interactions.
Nooren IM, Thornton JM.
J Mol Biol Volume 325 (2003) p.991-1018

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

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

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

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

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

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

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

Sequences and topology.
Gerstein M, Thornton JM.
Curr Opin Struct Biol Volume 13 (2003) p.341-343

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

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

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

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

Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases.
Zhang RG, Duke N, Laskowski R, Evdokimova E, Skarina T, Edwards A, Joachimiak A, Savchenko A.
Proteins Volume 51 (2003) p.311-314

Estimation of weights and validation: a marginal likelihood approach.
Lebedev AA, Tickle IJ, Laskowski RA, Moss DS.
Acta Crystallogr D Biol Crystallogr Volume 59 (2003) p.1557-1566

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

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

2002

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

Pathway evolution, structurally speaking.
Rison SC, Thornton JM.
Curr Opin Struct Biol Volume 12 (2002) p.374-382

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

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

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

Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.
Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Joachimiak A, Edwards A, Savchenko A.
Proteins Volume 48 (2002) p.427-430

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

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

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

Plasticity of enzyme active sites.
Todd AE, Orengo CA, Thornton JM.
Trends Biochem Sci Volume 27 (2002) p.419-426

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

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

Bioinformatics and protein design.
Laskowski RA, Chan AW.
Curr Pharm Biotechnol Volume 3 (2002) p.317-327

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

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

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

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

Sequence and structural differences between enzyme and nonenzyme homologs.
Todd AE, Orengo CA, Thornton JM.
Structure Volume 10 (2002) p.1435-1451

2001

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

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

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

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

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

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

Protein-protein interfaces: analysis of amino acid conservation in homodimers.
Valdar WS, Thornton JM.
Proteins Volume 42 (2001) p.108-124

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

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

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

From genome to function.
Thornton JM.
Science Volume 292 (2001) p.2095-2097

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

2000

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

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

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

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

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

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

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

Discriminating between homodimeric and monomeric proteins in the crystalline state.
Ponstingl H, Henrick K, Thornton JM.
Proteins Volume 41 (2000) p.47-57

1999

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

Evolution of protein function, from a structural perspective.
Todd AE, Orengo CA, Thornton JM.
Curr Opin Chem Biol Volume 3 (1999) p.548-556

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

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

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

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

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

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

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

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

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

From protein structure to function.
Orengo CA, Todd AE, Thornton JM.
Curr Opin Struct Biol Volume 9 (1999) p.374-382

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

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

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

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

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

1998

Validation of protein models derived from experiment.
Laskowski RA, MacArthur MW, Thornton JM.
Curr Opin Struct Biol Volume 8 (1998) p.631-639

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

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

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

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

Evolution of the androgen receptor: structure-function implications.
Thornton JW, Kelley DB.
Bioessays Volume 20 (1998) p.860-869

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

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

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

Contemporary approaches to protein structure classification.
Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM.
Bioessays Volume 20 (1998) p.884-891

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

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

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

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

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

Protein structure prediction.
Westhead DR, Thornton JM.
Curr Opin Biotechnol Volume 9 (1998) p.383-389

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

PQS: a protein quaternary structure file server.
Henrick K, Thornton JM.
Trends Biochem Sci Volume 23 (1998) p.358-361

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

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

1997

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

Assessment of comparative modeling in CASP2.
Martin AC, MacArthur MW, Thornton JM.
Proteins Volume Suppl 1 (1997) p.14-28

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

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

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

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

Non-randomness in side-chain packing: the distribution of interplanar angles.
Mitchell JB, Laskowski RA, Thornton JM.
Proteins Volume 29 (1997) p.370-380

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

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

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

1996

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Potential energy functions for threading.
Jones DT, Thornton JM.
Curr Opin Struct Biol Volume 6 (1996) p.210-216

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

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

1995

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

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

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

Protein-protein interactions: a review of protein dimer structures.
Jones S, Thornton JM.
Prog Biophys Mol Biol Volume 63 (1995) p.31-65

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

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

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

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

1994

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

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

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

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

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

NMR and crystallography--complementary approaches to structure determination.
MacArthur MW, Driscoll PC, Thornton JM.
Trends Biotechnol Volume 12 (1994) p.149-153

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

Protein superfamilies and domain superfolds.
Orengo CA, Jones DT, Thornton JM.
Nature Volume 372 (1994) p.631-634

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

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

A mutation data matrix for transmembrane proteins.
Jones DT, Taylor WR, Thornton JM.
FEBS Lett Volume 339 (1994) p.269-275