Enzyme function and evolution through the lens of bioinformatics.

Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

Nat Struct Mol Biol, 2022

doi:10.1038/s41594-022-00849-w.

Mapping the Constrained Coding Regions in the human genome to their corresponding proteins

Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM.

2022

doi:10.1101/2022.09.12.507545.

EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions

Ribeiro AJM, Riziotis IG, Tyzack JD, Borkakoti N, Thornton JM.

2022

doi:10.1101/2022.09.05.506575.

Capturing the geometry, function, and evolution of enzymes with 3D templates.

Riziotis IG, Thornton JM.

Protein Sci, 2022

doi:10.1002/pro.4363.

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs.

Santana CA, Izidoro SC, de Melo-Minardi RC, Tyzack JD, Ribeiro AJM, Pires DEV, Thornton JM, de A Silveira S.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkac323.

Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.

Riziotis IG, Ribeiro AJM, Borkakoti N, Thornton JM.

J Mol Biol, 2022

doi:10.1016/j.jmb.2022.167517.

The impact of AlphaFold2 one year on.

Jones DT, Thornton JM.

Nat Methods, 2022

doi:10.1038/s41592-021-01365-3.

PDBsum extras: SARS-CoV-2 and AlphaFold models.

Laskowski RA, Thornton JM.

Protein Sci, 2022

doi:10.1002/pro.4238.

PDBe-KB: collaboratively defining the biological context of structural data.

PDBe-KB consortium.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab988.

The Enzyme Portal: an integrative tool for enzyme information and analysis.

Zaru R, Onwubiko J, Ribeiro AJM, Cochrane K, Tyzack JD, Muthukrishnan V, Pravda L, Thornton JM, O'Donovan C, Velanker S, Orchard S, Leach A, Martin MJ.

FEBS J, 2022

doi:10.1111/febs.16168.

Conformational variation in enzyme catalysis: A structural study on catalytic residues

Riziotis IG, Ribeiro AJM, Borkakoti N, Thornton JM.

2021

doi:10.1101/2021.12.12.472283.

AlphaFold heralds a data-driven revolution in biology and medicine.

Thornton JM, Laskowski RA, Borkakoti N.

Nat Med, 2021

doi:10.1038/s41591-021-01533-0.

A structural biology community assessment of AlphaFold 2 applications

Akdel M, Pires DEV, Porta Pardo E, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Ruiz Serra V, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Lindorff-Larsen K, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

2021

doi:10.1101/2021.09.26.461876.

A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.

Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM.

Sci Rep, 2021

doi:10.1038/s41598-021-93715-6.

Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders.

Ochoa R, Laskowski RA, Thornton JM, Cossio P.

Front Mol Biosci, 2021

doi:10.3389/fmolb.2021.636562.

Functional conservation in genes and pathways linking ageing and immunity.

Fabian DK, Fuentealba M, Dönertaş HM, Partridge L, Thornton JM.

Immun Ageing, 2021

doi:10.1186/s12979-021-00232-1.

Common genetic associations between age-related diseases.

Dönertaş HM, Fabian DK, Valenzuela MF, Partridge L, Thornton JM.

Nat Aging, 2021

doi:10.1038/s43587-021-00051-5.

Transposable Element Landscape in Drosophila Populations Selected for Longevity.

Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM.

Genome Biol Evol, 2021

doi:10.1093/gbe/evab031.

Cell type-specific modulation of healthspan by Forkhead family transcription factors in the nervous system.

Bolukbasi E, Woodling NS, Ivanov DK, Adcott J, Foley A, Rajasingam A, Gittings LM, Aleyakpo B, Niccoli T, Thornton JM, Partridge L.

Proc Natl Acad Sci U S A, 2021

doi:10.1073/pnas.2011491118.

Data-driven identification of ageing-related diseases from electronic health records.

Kuan V, Fraser HC, Hingorani M, Denaxas S, Gonzalez-Izquierdo A, Direk K, Nitsch D, Mathur R, Parisinos CA, Lumbers RT, Sofat R, Wong ICK, Casas JP, Thornton JM, Hemingway H, Partridge L, Hingorani AD.

Sci Rep, 2021

doi:10.1038/s41598-021-82459-y.

A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases and prostate cancer progression

Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM.

2021

doi:10.1101/2021.01.21.427605.

GRaSP: a graph-based residue neighborhood strategy to predict binding sites.

Santana CA, Silveira SA, Moraes JPA, Izidoro SC, de Melo-Minardi RC, Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM.

Bioinformatics, 2020

doi:10.1093/bioinformatics/btaa805.

An automated protocol for modelling peptide substrates to proteases.

Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM.

BMC Bioinformatics, 2020

doi:10.1186/s12859-020-03931-6.

Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila.

Bjedov I, Cochemé HM, Foley A, Wieser D, Woodling NS, Castillo-Quan JI, Norvaisas P, Lujan C, Regan JC, Toivonen JM, Murphy MP, Thornton J, Kinghorn KJ, Neufeld TP, Cabreiro F, Partridge L.

PLoS Genet, 2020

doi:10.1371/journal.pgen.1009083.

A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data.

Ivanov DK, Bostelmann G, Lan-Leung B, Williams J, Partridge L, Escott-Price V, Thornton JM.

PLoS One, 2020

doi:10.1371/journal.pone.0240824.

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice

Fuentealba M, Fabian DK, Dönertaş HM, Thornton JM, Partridge L.

2020

doi:10.1101/2020.10.20.347013.

In conversation with Janet Thornton.

Dhillon P, Thornton JM.

FEBS J, 2020

doi:10.1111/febs.15567.

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).

Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B.

F1000Res, 2020

doi:10.12688/f1000research.20559.1.

Common genetic associations between age-related diseases

Dönertaş HM, Fabian DK, Valenzuela MF, Partridge L, Thornton JM.

2020

doi:10.1101/2020.06.16.20132621.

Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate.

Sanchis-Juan A, Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, NIHR BioResource, Carss KJ, Thornton J, Raymond FL.

Mol Genet Genomic Med, 2020

doi:10.1002/mgg3.1106.

Temporal changes in the gene expression heterogeneity during brain development and aging.

Işıldak U, Somel M, Thornton JM, Dönertaş HM.

Sci Rep, 2020

doi:10.1038/s41598-020-60998-0.

A global analysis of function and conservation of catalytic residues in enzymes.

Ribeiro AJM, Tyzack JD, Borkakoti N, Holliday GL, Thornton JM.

J Biol Chem, 2020

doi:10.1074/jbc.rev119.006289.

Identifying pseudoenzymes using functional annotation: pitfalls of common practice.

Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM.

FEBS J, 2020

doi:10.1111/febs.15142.

VarSite: Disease variants and protein structure.

Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA, Thornton JM.

Protein Sci, 2020

doi:10.1002/pro.3746.

PDBe-KB: a community-driven resource for structural and functional annotations.

PDBe-KB consortium.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz853.

Transposable element landscape inDrosophilapopulations selected for longevity

Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM.

2019

doi:10.1101/867838.

Exploring Chemical Biosynthetic Design Space with Transform-MinER.

Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM.

ACS Synth Biol, 2019

doi:10.1021/acssynbio.9b00105.

Emerging concepts in pseudoenzyme classification, evolution, and signaling.

Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA.

Sci Signal, 2019

doi:10.1126/scisignal.aat9797.

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM.

Genome Biol, 2019

doi:10.1186/s13059-019-1753-9.

Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate

Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, Thornton J, Raymond FL, NIHR BioResource.

2019

doi:10.1101/678219.

VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.

Stephenson JD, Laskowski RA, Nightingale A, Hurles ME, Thornton JM.

Bioinformatics, 2019

doi:10.1093/bioinformatics/btz482.

The widespread increase in inter-individual variability of gene expression in the human brain with age.

Kedlian VR, Donertas HM, Thornton JM.

Aging (Albany NY), 2019

doi:10.18632/aging.101912.

Gene expression heterogeneity during brain development and aging: temporal changes and functional consequences

Işıldak U, Somel M, Thornton JM, Dönertaş HM.

2019

doi:10.1101/595249.

Finding enzyme cofactors in Protein Data Bank.

Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S.

Bioinformatics, 2019

doi:10.1093/bioinformatics/btz115.

Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1

Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Stegle O, Sadikovic B, Reik W, Thornton JM.

2019

doi:10.1101/545830.

The variability of expression of many genes and most functional pathways is observed to increase with age in brain transcriptome data

Kedlian VR, Donertas HM, Thornton JM.

2019

doi:10.1101/526491.

Using the drug-protein interactome to identify anti-ageing compounds for humans.

Fuentealba M, Dönertaş HM, Williams R, Labbadia J, Thornton JM, Partridge L.

PLoS Comput Biol, 2019

doi:10.1371/journal.pcbi.1006639.

Identifying Potential Ageing-Modulating Drugs In Silico.

Dönertaş HM, Fuentealba M, Partridge L, Thornton JM.

Trends Endocrinol Metab, 2019

doi:10.1016/j.tem.2018.11.005.

CATH: expanding the horizons of structure-based functional annotations for genome sequences.

Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, Tolulope A, Scholes HM, Senatorov I, Bujan A, Ceballos Rodriguez-Conde F, Dowling B, Thornton J, Orengo CA.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky1097.

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.

Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM.

Methods Mol Biol, 2019

doi:10.1007/978-1-4939-8736-8_14.

Using the drug-protein interactome to identify anti-ageing compounds for humans

Fuentealba Valenzuela M, Melike Dönertaş H, Williams R, Labbadia J, Thornton J, Partridge L.

2018

doi:10.1101/438234.

Gene Expression-Based Drug Repurposing to Target Ageing

Dönertaş HM, Valenzuela MF, Partridge L, Thornton JM.

2018

doi:10.1101/253344.

Gene expression-based drug repurposing to target aging.

Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM.

Aging Cell, 2018

doi:10.1111/acel.12819.

Transform-MinER: transforming molecules in enzyme reactions.

Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM.

Bioinformatics, 2018

doi:10.1093/bioinformatics/bty394.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.

Tyzack JD, Fernando L, Ribeiro AJM, Borkakoti N, Thornton JM.

Structure, 2018

doi:10.1016/j.str.2018.02.009.

To what extent do structural changes in catalytic metal sites affect enzyme function?

Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C.

J Inorg Biochem, 2018

doi:10.1016/j.jinorgbio.2017.11.002.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM.

Nucleic Acids Res, 2018

doi:10.1093/nar/gkx1012.

PDBsum: Structural summaries of PDB entries.

Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM.

Protein Sci, 2018

doi:10.1002/pro.3289.

Editorial overview: Catalysis and regulation.

Thornton J, Orengo C.

Curr Opin Struct Biol, 2017

doi:10.1016/j.sbi.2017.11.005.

Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.

Bolukbasi E, Khericha M, Regan JC, Ivanov DK, Adcott J, Dyson MC, Nespital T, Thornton JM, Alic N, Partridge L.

Cell Rep, 2017

doi:10.1016/j.celrep.2017.09.042.

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkx814.

Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.

Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, DDD Study, Wright CF.

Mol Genet Genomic Med, 2017

doi:10.1002/mgg3.304.

Understanding enzyme function evolution from a computational perspective.

Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM.

Curr Opin Struct Biol, 2017

doi:10.1016/j.sbi.2017.08.003.

Drug repurposing for aging research using model organisms.

Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM.

Aging Cell, 2017

doi:10.1111/acel.12626.

Anna Tramontano 1957-2017.

Thornton JM, Valencia A, Schwede T.

Nat Struct Mol Biol, 2017

doi:10.1038/nsmb.3410.

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.

Kerr F, Sofola-Adesakin O, Ivanov DK, Gatliff J, Gomez Perez-Nievas B, Bertrand HC, Martinez P, Callard R, Snoeren I, Cochemé HM, Adcott J, Khericha M, Castillo-Quan JI, Wells G, Noble W, Thornton J, Partridge L.

PLoS Genet, 2017

doi:10.1371/journal.pgen.1006593.

Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.

Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF.

Hum Mol Genet, 2017

doi:10.1093/hmg/ddw409.

Drug repurposing for ageing research using model organisms

Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM.

2016

doi:10.1101/095380.

Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.

Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA.

J Mol Biol, 2016

doi:10.1016/j.jmb.2016.07.003.

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM.

Bioinformatics, 2016

doi:10.1093/bioinformatics/btw096.

Exploring the chemistry and evolution of the isomerases.

Martínez Cuesta S, Rahman SA, Thornton JM.

Proc Natl Acad Sci U S A, 2016

doi:10.1073/pnas.1509494113.

Characterising Complex Enzyme Reaction Data.

Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM.

PLoS One, 2016

doi:10.1371/journal.pone.0147952.

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.

Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study, Wright CF.

Hum Mol Genet, 2016

doi:10.1093/hmg/ddv625.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA.

J Mol Biol, 2016

doi:10.1016/j.jmb.2015.11.010.

Characterising Complex Enzyme Reaction Data

Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM.

2015

doi:10.1101/028142.

Proteins: interaction at a distance.

Laskowski RA, Thornton JM.

IUCrJ, 2015

doi:10.1107/s2052252515020217.

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.

Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N.

PLoS Comput Biol, 2015

doi:10.1371/journal.pcbi.1004546.

The history of the CATH structural classification of protein domains.

Sillitoe I, Dawson N, Thornton J, Orengo C.

Biochimie, 2015

doi:10.1016/j.biochi.2015.08.004.

SurvCurv database and online survival analysis platform update.

Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM.

Bioinformatics, 2015

doi:10.1093/bioinformatics/btv463.

The new science of ageing.

Partridge L, Thornton J, Bates G.

Philos Trans R Soc Lond B Biol Sci, 2015

doi:10.1098/rstb.2015.0249.

The Classification and Evolution of Enzyme Function.

Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM.

Biophys J, 2015

doi:10.1016/j.bpj.2015.04.020.

Longevity GWAS Using the Drosophila Genetic Reference Panel.

Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM.

J Gerontol A Biol Sci Med Sci, 2015

doi:10.1093/gerona/glv047.

What you need to know to make the most of big data in biology.

Thornton J.

Lancet, 2015

doi:10.1016/s0140-6736(15)60321-x.

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, 2015

doi:10.1093/nar/gku947.

The NAD Binding Domain and the Short Chain Dehydrogenase/Reductase (SDR) Superfamily

Furnham N, Holliday GL, Thornton JM.

2014

doi:.

Delivering ICT Infrastructure for Biomedical Research

Rahman SA, Furnham N, Holliday GL and Thornton JM.

Nat Methods, 2014

doi:.

Databases and data sources: EBI and ELIXIR

Crosswell LC, Thornton JM.

2014

doi:.

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.

Papatheodorou I, Petrovs R, Thornton JM.

Bioinformatics, 2014

doi:10.1093/bioinformatics/btu493.

The evolution of enzyme function in the isomerases.

Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM.

Curr Opin Struct Biol, 2014

doi:10.1016/j.sbi.2014.06.002.

Exploring the biological and chemical complexity of the ligases.

Holliday GL, Rahman SA, Furnham N, Thornton JM.

J Mol Biol, 2014

doi:10.1016/j.jmb.2014.03.008.

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), 2014

doi:10.18632/aging.100638.

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, 2014

doi:10.1371/journal.pgen.1004109.

EC-BLAST: a tool to automatically search and compare enzyme reactions.

Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.

Nat Methods, 2014

doi:10.1038/nmeth.2803.

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, 2014

doi:10.1093/nar/gkt1243.

The European Bioinformatics Institute's data resources 2014.

Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1206.

PDBsum additions.

de Beer TA, Berka K, Thornton JM, Laskowski RA.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt940.

Protein Data Resources

Furnham N, Garavelli JS, Thornton JM.

2013

doi:.

The Ramachandran Plot and Protein Structure Validation

Laskowski RA, Furnham N, Thornton JM.

2013

doi:.

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, 2013

doi:10.1371/journal.pcbi.1003382.

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, 2013

doi:10.1107/s0907444913022294.

The Ramachandran plot and protein structure validation

Laskowski RA, Furnham N, Thornton JM.

2013

doi:10.1142/9789814449144_0005.

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.

Ziehm M, Thornton JM.

Aging Cell, 2013

doi:10.1111/acel.12121.

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.

Ziehm M, Piper MD, Thornton JM.

Aging Cell, 2013

doi:10.1111/acel.12123.

Elucidating human phosphatase-substrate networks.

Li X, Wilmanns M, Thornton J, Köhn M.

Sci Signal, 2013

doi:10.1126/scisignal.2003203.

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, 2013

doi:10.1039/c3mb25485b.

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, 2013

doi:10.1093/nar/gks1211.

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, 2013

doi:10.1093/nar/gks1112.

Abstracting knowledge from the Protein Data Bank.

Furnham N, Laskowski RA, Thornton JM.

Biopolymers, 2013

doi:10.1002/bip.22107.

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.

2012

doi:.

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, 2012

doi:10.1038/nrd3503-c2.

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, 2012

doi:10.1371/journal.pone.0050881.

Current challenges in genome annotation through structural biology and bioinformatics.

Furnham N, de Beer TA, Thornton JM.

Curr Opin Struct Biol, 2012

doi:10.1016/j.sbi.2012.07.005.

ELIXIR: a distributed infrastructure for European biological data.

Crosswell LC, Thornton JM.

Trends Biotechnol, 2012

doi:10.1016/j.tibtech.2012.02.002.

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, 2012

doi:10.1371/journal.pone.0033101.

Women in science.

Dean C, Osborn M, Oshlack A, Thornton J.

Genome Biol, 2012

doi:10.1186/gb-2012-13-3-148.

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, 2012

doi:10.1371/journal.pcbi.1002403.

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, 2012

doi:10.1093/nar/gkr852.

Celebrating structural biology.

Nat Struct Mol Biol, 2011

doi:10.1038/nsmb1211-1304.

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, 2011

doi:10.1038/nrd3503.

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, 2011

doi:10.1021/bi201095z.

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, 2011

doi:10.1038/msb.2011.36.

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, 2011

doi:10.1111/j.1742-4658.2011.08190.x.

1,000 structures and more from the MCSG.

Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA.

BMC Struct Biol, 2011

doi:10.1186/1472-6807-11-2.

Computational biology for ageing.

Wieser D, Papatheodorou I, Ziehm M, Thornton JM.

Philos Trans R Soc Lond B Biol Sci, 2011

doi:10.1098/rstb.2010.0286.

The new science of ageing.

Partridge L, Thornton J, Bates G.

Philos Trans R Soc Lond B Biol Sci, 2011

doi:10.1098/rstb.2010.0298.

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, 2011

doi:10.1093/nar/gkq1001.

The structures and physicochemical properties of organic cofactors in biocatalysis.

Fischer JD, Holliday GL, Rahman SA, Thornton JM.

J Mol Biol, 2010

doi:10.1016/j.jmb.2010.09.018.

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, 2010

doi:10.1038/msb.2010.54.

The CoFactor database: organic cofactors in enzyme catalysis.

Fischer JD, Holliday GL, Thornton JM.

Bioinformatics, 2010

doi:10.1093/bioinformatics/btq442.

Heme proteins--diversity in structural characteristics, function, and folding.

Smith LJ, Kahraman A, Thornton JM.

Proteins, 2010

doi:10.1002/prot.22747.

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, 2010

doi:10.1371/journal.pgen.1000881.

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, 2010

doi:10.1073/pnas.0910632107.

The European Bioinformatics Institute's data resources.

Brooksbank C, Cameron G, Thornton J.

Nucleic Acids Res, 2010

doi:10.1093/nar/gkp986.

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, 2010

doi:10.1002/prot.22633.

Domain-ligand mapping for enzymes.

Bashton M, Thornton JM.

J Mol Recognit, 2010

doi:10.1002/jmr.992.

The (non)malignancy of cancerous amino acidic substitutions.

Talavera D, Taylor MS, Thornton JM.

Proteins, 2010

doi:10.1002/prot.22574.

Protein Evolution – Sequence, Structure and Systems

Sternberg M, Thornton J, Laskowski R.

2009

doi:.

Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease

Watson JD, Thornton JM.

2009

doi:10.1007/978-90-481-2339-1_13.

New open drug activity data at EBI

Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J.

Chem Cent J, 2009

doi:10.1186/1752-153x-3-s1-o3.

Small Molecule Subgraph Detector (SMSD) toolkit.

Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.

J Cheminform, 2009

doi:10.1186/1758-2946-1-12.

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, 2009

doi:10.1371/journal.pcbi.1000585.

Mapping human metabolic pathways in the small molecule chemical space.

Macchiarulo A, Thornton JM, Nobeli I.

J Chem Inf Model, 2009

doi:10.1021/ci900196u.

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, 2009

doi:10.1126/science.1177221.

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.

Oliva R, Thornton JM, Pellegrini-Calace M.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp545.

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, 2009

doi:10.1038/461168a.

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, 2009

doi:10.1016/j.str.2009.06.015.

Missing in action: enzyme functional annotations in biological databases.

Furnham N, Garavelli JS, Apweiler R, Thornton JM.

Nat Chem Biol, 2009

doi:10.1038/nchembio0809-521.

The fine details of evolution.

Laskowski RA, Thornton JM, Sternberg MJ.

Biochem Soc Trans, 2009

doi:10.1042/bst0370723.

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, 2009

doi:10.1371/journal.pcbi.1000440.

Understanding the functional roles of amino acid residues in enzyme catalysis.

Holliday GL, Mitchell JB, Thornton JM.

J Mol Biol, 2009

doi:10.1016/j.jmb.2009.05.015.

Metal-MACiE: a database of metals involved in biological catalysis.

Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp256.

The structural basis of allosteric regulation in proteins.

Laskowski RA, Gerick F, Thornton JM.

FEBS Lett, 2009

doi:10.1016/j.febslet.2009.03.019.

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, 2009

doi:10.1016/j.jmb.2009.02.052.

WSsas: a web service for the annotation of functional residues through structural homologues.

Talavera D, Laskowski RA, Thornton JM.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp116.

Annotations for all by all - the BioSapiens network.

Thornton J, BioSapiens Network.

Genome Biol, 2009

doi:10.1186/gb-2009-10-2-401.

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, 2009

doi:10.1186/gb-2009-10-2-207.

Protein promiscuity and its implications for biotechnology.

Nobeli I, Favia AD, Thornton JM.

Nat Biotechnol, 2009

doi:10.1038/nbt1519.

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, 2009

doi:10.1016/j.cbi.2008.10.040.

Genome and proteome annotation: organization, interpretation and integration.

Reeves GA, Talavera D, Thornton JM.

J R Soc Interface, 2009

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, 2009

doi:10.1093/nar/gkn877.

Methods to Characterize the Structure of Enzyme Binding Sites

Kahraman A and Thornton JM.

2008

doi:.

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, 2008

doi:10.1093/bioinformatics/btn528.

Metabolic innovations towards the human lineage.

Freilich S, Goldovsky L, Ouzounis CA, Thornton JM.

BMC Evol Biol, 2008

doi:10.1186/1471-2148-8-247.

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Najmanovich R, Kurbatova N, Thornton J.

Bioinformatics, 2008

doi:10.1093/bioinformatics/btn263.

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, 2008

doi:10.1007/s00775-008-0404-5.

Understanding the molecular machinery of genetics through 3D structures.

Laskowski RA, Thornton JM.

Nat Rev Genet, 2008

doi:10.1038/nrg2273.

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.

Favia AD, Nobeli I, Glaser F, Thornton JM.

J Mol Biol, 2008

doi:10.1016/j.jmb.2007.10.065.

Evolution of binding sites for zinc and calcium ions playing structural roles.

Torrance JW, Macarthur MW, Thornton JM.

Proteins, 2008

doi:10.1002/prot.21741.

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, 2008

doi:10.1096/fj.07-9261com.

PROCOGNATE: a cognate ligand domain mapping for enzymes.

Bashton M, Nobeli I, Thornton JM.

Nucleic Acids Res, 2008

doi:10.1093/nar/gkm611.

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands

Kahraman A, Morris R, Laskowski R, Thornton J.

BMC Bioinformatics, 2007

doi:.

Evolving Methods for Macromolecular Crystallography

Watson J, Golovin A, Laskowski R, Henrick K, Thornton JM, Joachimiak A and Edwards A.

2007

doi:.

Variation of geometrical and phsicochemical properties in protein binding pockets and their ligands

Kahraman A, Morris RJ, Laskowski RA, Thornton JM.

2007

doi:.

Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

PLoS Biol, 2007

doi:.

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, 2007

doi:10.1371/journal.pcbi.0030206.

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.

Ward JJ, Thornton JM.

PLoS Comput Biol, 2007

doi:10.1371/journal.pcbi.0030198.

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, 2007

doi:10.1039/b703107f.

The chemistry of protein catalysis.

Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.

J Mol Biol, 2007

doi:10.1016/j.jmb.2007.07.034.

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, 2007

doi:10.1186/gb-2007-8-7-r132.

Estimation and correction of non-specific binding in a large-scale spike-in experiment.

Schuster EF, Blanc E, Partridge L, Thornton JM.

Genome Biol, 2007

doi:10.1186/gb-2007-8-6-r126.

Correcting for sequence biases in present/absent calls.

Schuster EF, Blanc E, Partridge L, Thornton JM.

Genome Biol, 2007

doi:10.1186/gb-2007-8-6-r125.

The geometry of interactions between catalytic residues and their substrates.

Torrance JW, Holliday GL, Mitchell JB, Thornton JM.

J Mol Biol, 2007

doi:10.1016/j.jmb.2007.03.055.

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, 2007

doi:10.1371/journal.pbio.0050097.

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, 2007

doi:10.1073/pnas.0700800104.

Shape variation in protein binding pockets and their ligands.

Kahraman A, Morris RJ, Laskowski RA, Thornton JM.

J Mol Biol, 2007

doi:10.1016/j.jmb.2007.01.086.

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, 2007

doi:10.1016/j.jmb.2007.01.063.

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, 2007

doi:10.1093/bioinformatics/btl292.

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, 2007

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, 2007

doi:10.1093/nar/gkl774.

Introduction. Bioinformatics: From Molecules to Systems

Jones DT, Sternberg MJE, Thornton JM.

2006

doi:.

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, 2006

doi:10.1016/j.mad.2006.10.002.

Cognate ligand domain mapping for enzymes.

Bashton M, Nobeli I, Thornton JM.

J Mol Biol, 2006

doi:10.1016/j.jmb.2006.09.041.

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, 2006

doi:10.1186/gb-2006-7-10-r89.

Protein superfamily evolution and the last universal common ancestor (LUCA).

Ranea JA, Sillero A, Thornton JM, Orengo CA.

J Mol Evol, 2006

doi:10.1007/s00239-005-0289-7.

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, 2006

doi:10.1107/s090744490602991x.

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, 2006

doi:10.1152/physiolgenomics.00084.2006.

Integrating biological data through the genome.

Reeves GA, Thornton JM, BioSapiens Network of Excellence.

Hum Mol Genet, 2006

doi:10.1093/hmg/ddl086.

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.

Whamond GS, Thornton JM.

J Mol Biol, 2006

doi:10.1016/j.jmb.2006.03.029.

A bioinformatician's view of the metabolome.

Nobeli I, Thornton JM.

Bioessays, 2006

doi:10.1002/bies.20414.

Introduction. Bioinformatics: from molecules to systems.

Jones DT, Sternberg MJ, Thornton JM.

Philos Trans R Soc Lond B Biol Sci, 2006

doi:10.1098/rstb.2005.1811.

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, 2006

doi:10.1016/j.mad.2006.01.006.

Conformational diversity of ligands bound to proteins.

Stockwell GR, Thornton JM.

J Mol Biol, 2006

doi:10.1016/j.jmb.2005.12.012.

A method for localizing ligand binding pockets in protein structures.

Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.

Proteins, 2006

doi:10.1002/prot.20769.

Binding pocket shape analysis for protein function prediction

Morris RJ, Kahraman A, Funkhouser T, Najmanovich R, Stockwell G, Glaser F, Laskowski R, Thornton JM.

2005

doi:.

Shape-based classification of bound ligands

Funkhouser T, Glaser F, Laskowski R, Morris RJ, Najmanovich R, Stockwell G, Thornton JM.

2005

doi:.

Prediction of Protein Function from Structure: Insights from Methods for the Detection of Local Structural Similarities

Najmanovich RF, Torrance JW, Thornton JM.

Biotechniques, 2005

doi:10.2144/05386te01.

Binding Pocket Shape Analysis for Protein Function Prediction

Morris RJ, Kahraman A, Thornton JM.

Acta Crystallogr, 2005

doi:.

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, 2005

doi:10.1074/jbc.m509187200.

Understanding nature's catalytic toolkit.

Gutteridge A, Thornton JM.

Trends Biochem Sci, 2005

doi:10.1016/j.tibs.2005.09.006.

MACiE: a database of enzyme reaction mechanisms.

Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB.

Bioinformatics, 2005

doi:10.1093/bioinformatics/bti693.

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, 2005

doi:10.1073/pnas.0504833102.

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, 2005

doi:10.1093/bioinformatics/bti575.

Protein function prediction using local 3D templates.

Laskowski RA, Watson JD, Thornton JM.

J Mol Biol, 2005

doi:10.1016/j.jmb.2005.05.067.

Protein families and their evolution-a structural perspective.

Orengo CA, Thornton JM.

Annu Rev Biochem, 2005

doi:10.1146/annurev.biochem.74.082803.133029.

Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.

Shanahan HP, Thornton JM.

Biopolymers, 2005

doi:10.1002/bip.20295.

Prediction of protein function from structure: insights from methods for the detection of local structural similarities.

Najmanovich RJ, Torrance JW, Thornton JM.

Biotechniques, 2005

doi:10.2144/05386te01.

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, 2005

doi:10.1186/gb-2005-6-7-r56.

ProFunc: a server for predicting protein function from 3D structure.

Laskowski RA, Watson JD, Thornton JM.

Nucleic Acids Res, 2005

doi:10.1093/nar/gki414.

Predicting protein function from sequence and structural data.

Watson JD, Laskowski RA, Thornton JM.

Curr Opin Struct Biol, 2005

doi:10.1016/j.sbi.2005.04.003.

The complement of enzymatic sets in different species.

Freilich S, Spriggs RV, George RA, Al-Lazikani B, Swindells M, Thornton JM.

J Mol Biol, 2005

doi:10.1016/j.jmb.2005.04.027.

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, 2005

doi:10.1093/bioinformatics/bti337.

Morphological aspects of oligomeric protein structures.

Ponstingl H, Kabir T, Gorse D, Thornton JM.

Prog Biophys Mol Biol, 2005

doi:10.1016/j.pbiomolbio.2004.07.010.

Progress of structural genomics initiatives: an analysis of solved target structures.

Todd AE, Marsden RL, Thornton JM, Orengo CA.

J Mol Biol, 2005

doi:10.1016/j.jmb.2005.03.037.

Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.

Pellegrini-Calace M, Thornton JM.

Nucleic Acids Res, 2005

doi:10.1093/nar/gki349.

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, 2005

doi:10.1016/j.jmb.2005.01.044.

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, 2005

doi:10.1016/j.jmb.2005.01.061.

Microeconomic principles explain an optimal genome size in bacteria.

Ranea JA, Grant A, Thornton JM, Orengo CA.

Trends Genet, 2005

doi:10.1016/j.tig.2004.11.014.

Conformational changes observed in enzyme crystal structures upon substrate binding.

Gutteridge A, Thornton J.

J Mol Biol, 2005

doi:10.1016/j.jmb.2004.11.013.

The European Bioinformatics Institute's data resources: towards systems biology.

Brooksbank C, Cameron G, Thornton J.

Nucleic Acids Res, 2005

doi:10.1093/nar/gki026.

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, 2005

doi:10.1093/nar/gki001.

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, 2005

doi:10.1093/nar/gki024.

The Metabolome

Nobeli I, Thornton JM.

2004

doi:.

The Proteome and the Metabolome: A Structural Perspective

Nobeli I, Thornton JM.

2004

doi:.

Conformational Change in Substrate Binding, Catalysis and Product Release: An Open and Shut Case?

Gutteridge A, Thornton JM.

FEBS Lett, 2004

doi:.

Software Engineering Challenges in Bioinformatics

Barker J, Thornton JM.

ICSE, 2004

doi:.

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, 2004

doi:10.1093/protein/gzh072.

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, 2004

doi:10.1093/bioinformatics/bth240.

An examination of the conservation of surface patch polarity for proteins.

Shanahan HP, Thornton JM.

Bioinformatics, 2004

doi:10.1093/bioinformatics/bth218.

Toward the detection and validation of repeats in protein structure.

Murray KB, Taylor WR, Thornton JM.

Proteins, 2004

doi:10.1002/prot.20202.

Ligand selectivity and competition between enzymes in silico.

Macchiarulo A, Nobeli I, Thornton JM.

Nat Biotechnol, 2004

doi:10.1038/nbt999.

SCOPEC: a database of protein catalytic domains.

George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB.

Bioinformatics, 2004

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, 2004

doi:10.1093/nar/gkh028.

Identifying DNA-binding proteins using structural motifs and the electrostatic potential.

Shanahan HP, Garcia MA, Jones S, Thornton JM.

Nucleic Acids Res, 2004

doi:10.1093/nar/gkh803.

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, 2004

doi:10.1038/ng0904-925.

Conformational change in substrate binding, catalysis and product release: an open and shut case?

Gutteridge A, Thornton J.

FEBS Lett, 2004

doi:10.1016/j.febslet.2004.03.067.

Evolution of protein superfamilies and bacterial genome size.

Ranea JA, Buchan DW, Thornton JM, Orengo CA.

J Mol Biol, 2004

doi:10.1016/j.jmb.2003.12.044.

Searching for functional sites in protein structures.

Jones S, Thornton JM.

Curr Opin Chem Biol, 2004

doi:10.1016/j.cbpa.2003.11.001.

Diversity of Protein-Protein Interactions

Nooren I, Thornton JM.

2003

doi:.

Protein-DNA Interactions: The Story so Far and a new method for prediction

Jones S, Thornton JM.

2003

doi:.

The Proteome and the Metabolome

Thornton JM, Nobeli I.

Biopolymers, 2003

doi:.

Proteomics: The Protein Complement of the Genome

Ponstingl H, Thornton JM.

Biochem (Lond), 2003

doi:.

Protein-DNA interactions: the story so far and a new method for prediction.

Jones S, Thornton JM.

Comp Funct Genomics, 2003

doi:10.1002/cfg.303.

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

Jones S, Shanahan HP, Berman HM, Thornton JM.

Nucleic Acids Res, 2003

doi:10.1093/nar/gkg922.

Inferring protein function from structure.

Bartlett GJ, Todd AE, Thornton JM.

Methods Biochem Anal, 2003

doi:.

The CATH domain structure database.

Orengo CA, Pearl FM, Thornton JM.

Methods Biochem Anal, 2003

doi:10.1002/0471721204.ch13.

From protein structure to biochemical function?

Laskowski RA, Watson JD, Thornton JM.

J Struct Funct Genomics, 2003

doi:10.1023/a:1026127927612.

A structure-based anatomy of the E.coli metabolome.

Nobeli I, Ponstingl H, Krissinel EB, Thornton JM.

J Mol Biol, 2003

doi:10.1016/j.jmb.2003.10.008.

Structural characterisation and functional significance of transient protein-protein interactions.

Nooren IM, Thornton JM.

J Mol Biol, 2003

doi:10.1016/s0022-2836(02)01281-0.

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, 2003

doi:10.1093/nar/gkg051.

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, 2003

doi:10.1093/nar/gkg062.

A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks.

Shepherd AJ, Gorse D, Thornton JM.

Proteins, 2003

doi:10.1002/prot.10290.

Recognizing the fold of a protein structure.

Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C.

Bioinformatics, 2003

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, 2003

doi:10.1093/bioinformatics/btg226.

Molecular basis of inherited diseases: a structural perspective.

Steward RE, MacArthur MW, Laskowski RA, Thornton JM.

Trends Genet, 2003

doi:10.1016/s0168-9525(03)00195-1.

Analysis of metabolic networks using a pathway distance metric through linear programming.

Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG.

Metab Eng, 2003

doi:10.1016/s1096-7176(03)00043-0.

Catalysing new reactions during evolution: economy of residues and mechanism.

Bartlett GJ, Borkakoti N, Thornton JM.

J Mol Biol, 2003

doi:10.1016/s0022-2836(03)00734-4.

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, 2003

doi:10.1080/1521654031000123385.

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, 2003

doi:10.1002/prot.10421.

Diversity of protein-protein interactions.

Nooren IM, Thornton JM.

EMBO J, 2003

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, 2003

doi:10.1016/s0022-2836(03)00515-1.

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, 2003

doi:10.1074/jbc.m303867200.

Sequences and topology.

Gerstein M, Thornton JM.

Curr Opin Struct Biol, 2003

doi:10.1016/s0959-440x(03)00080-0.

Using structural motif templates to identify proteins with DNA binding function.

Jones S, Barker JA, Nobeli I, Thornton JM.

Nucleic Acids Res, 2003

doi:10.1093/nar/gkg386.

Proteins, Small Molecules and Networks

Nobeli I, Thornton JM.

2002

doi:.

PROCHECK: Validation of Protein Structure Coordinates

Laskowski RA, MacArthur MW, Thornton JM.

2002

doi:.

Automatic Interence of Protein Quatenary Structure from Crystals

Ponstingl H, Kabir T, Thornton JM.

J Appl Crystallogr, 2002

doi:.

Analysis of catalytic residues in enzyme active sites.

Bartlett GJ, Porter CT, Borkakoti N, Thornton JM.

J Mol Biol, 2002

doi:10.1016/s0022-2836(02)01036-7.

Quantifying the similarities within fold space.

Harrison A, Pearl F, Mott R, Thornton J, Orengo C.

J Mol Biol, 2002

doi:10.1016/s0022-2836(02)00992-0.

Sequence and structural differences between enzyme and nonenzyme homologs.

Todd AE, Orengo CA, Thornton JM.

Structure, 2002

doi:10.1016/s0969-2126(02)00861-4.

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, 2002

doi:10.1016/s0022-2836(02)00649-6.

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, 2002

doi:10.1073/pnas.162376199.

Plasticity of enzyme active sites.

Todd AE, Orengo CA, Thornton JM.

Trends Biochem Sci, 2002

doi:10.1016/s0968-0004(02)02158-8.

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.

Luscombe NM, Thornton JM.

J Mol Biol, 2002

doi:10.1016/s0022-2836(02)00571-5.

Pathway evolution, structurally speaking.

Rison SC, Thornton JM.

Curr Opin Struct Biol, 2002

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, 2002

doi:10.1002/prot.10152.

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.

Rison SC, Teichmann SA, Thornton JM.

J Mol Biol, 2002

doi:10.1016/s0022-2836(02)00140-7.

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, 2002

doi:10.1038/nsb0602-416.

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, 2002

doi:10.1091/mbc.01-09-0473.

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, 2002

doi:10.1101/gr.213802.

Wavelet transforms for the characterization and detection of repeating motifs.

Murray KB, Gorse D, Thornton JM.

J Mol Biol, 2002

doi:10.1006/jmbi.2001.5332.

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, 2002

doi:10.1002/humu.10032.

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, 2002

doi:10.1002/1615-9861(200201)2:1<11::aid-prot11>3.0.co;2-t.

Playing with Proteins

Thornton JM.

2001

doi:.

Structural Genomics Takes off

Thornton JM.

2001

doi:.

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, 2001

doi:10.1002/jcc.1036.

Conservation helps to identify biologically relevant crystal contacts.

Valdar WS, Thornton JM.

J Mol Biol, 2001

doi:10.1006/jmbi.2001.5034.

The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.

Nagano N, Porter CT, Thornton JM.

Protein Eng, 2001

doi:10.1093/protein/14.11.845.

Small-molecule metabolism: an enzyme mosaic.

Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C.

Trends Biotechnol, 2001

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, 2001

doi:10.1093/nar/29.21.4294.

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, 2001

doi:10.1006/jmbi.2001.4912.

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, 2001

doi:10.1093/nar/29.13.2860.

From genome to function.

Thornton JM.

Science, 2001

doi:10.1126/science.292.5524.2095.

Structural genomics takes off.

Thornton J.

Trends Biochem Sci, 2001

doi:10.1016/s0968-0004(00)01765-5.

Evolution of function in protein superfamilies, from a structural perspective.

Todd AE, Orengo CA, Thornton JM.

J Mol Biol, 2001

doi:10.1006/jmbi.2001.4513.

The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution.

Thornton JM.

Protein Sci, 2001

doi:10.1110/ps.90001.

Protein-RNA interactions: a structural analysis.

Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM.

Nucleic Acids Res, 2001

doi:10.1093/nar/29.4.943.

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, 2001

doi:10.1093/nar/29.1.223.

Protein-protein interfaces: analysis of amino acid conservation in homodimers.

Valdar WS, Thornton JM.

Proteins, 2001

doi:10.1002/1097-0134(20010101)42:1<108::aid-prot110>3.0.co;2-o.

Comparison of functional annotation schemes for genomes.

Rison SC, Hodgman TC, Thornton JM.

Funct Integr Genomics, 2000

doi:10.1007/s101420000005.

An overview of the structures of protein-DNA complexes.

Luscombe NM, Austin SE, Berman HM, Thornton JM.

Genome Biol, 2000

doi:10.1186/gb-2000-1-1-reviews001.

From structure to function: approaches and limitations.

Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA.

Nat Struct Biol, 2000

doi:10.1038/80784.

Discriminating between homodimeric and monomeric proteins in the crystalline state.

Ponstingl H, Henrick K, Thornton JM.

Proteins, 2000

doi:10.1002/1097-0134(20001001)41:1<47::aid-prot80>3.3.co;2-#.

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, 2000

doi:10.1042/bst0280269.

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, 2000

doi:10.1093/protein/13.3.153.

Analysis and prediction of carbohydrate binding sites.

Taroni C, Jones S, Thornton JM.

Protein Eng, 2000

doi:10.1093/protein/13.2.89.

Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.

Jones S, Marin A, Thornton JM.

Protein Eng, 2000

doi:10.1093/protein/13.2.77.

Assigning genomic sequences to CATH.

Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA.

Nucleic Acids Res, 2000

doi:10.1093/nar/28.1.277.

Software Tools for Protein Structure Analysis and Fold Classification

Thornton JM, Mitchie AD, Hutchinson EG, Laskowski RA, Orengo CA.

1999

doi:.

BLEEP - A Potential of Mean Force Describing Protein-Ligan Interactions: Generating the Potential

Mitchell JBO, Laskowski RA, Alex A, Thornton JM.

J Comput Chem, 1999

doi:.

Three-dimensional structure analysis of PROSITE patterns.

Kasuya A, Thornton JM.

J Mol Biol, 1999

doi:10.1006/jmbi.1999.2581.

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, 1999

doi:10.1093/nar/27.1.275.

Protein folds, functions and evolution.

Thornton JM, Orengo CA, Todd AE, Pearl FM.

J Mol Biol, 1999

doi:10.1006/jmbi.1999.3054.

Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.

Nagano N, Hutchinson EG, Thornton JM.

Protein Sci, 1999

doi:10.1110/ps.8.10.2072.

Evolution of protein function, from a structural perspective.

Todd AE, Orengo CA, Thornton JM.

Curr Opin Chem Biol, 1999

doi:10.1016/s1367-5931(99)00007-1.

From protein structure to function.

Orengo CA, Todd AE, Thornton JM.

Curr Opin Struct Biol, 1999

doi:10.1016/s0959-440x(99)80051-7.

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, 1999

doi:10.1093/protein/12.5.375.

Prediction of the location and type of beta-turns in proteins using neural networks.

Shepherd AJ, Gorse D, Thornton JM.

Protein Sci, 1999

doi:10.1110/ps.8.5.1045.

Motif-based searching in TOPS protein topology databases.

Gilbert D, Westhead D, Nagano N, Thornton J.

Bioinformatics, 1999

doi:10.1093/bioinformatics/15.4.317.

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, 1999

doi:10.1016/s0006-3495(99)77398-4.

Correlation of observed fold frequency with the occurrence of local structural motifs.

Salem GM, Hutchinson EG, Orengo CA, Thornton JM.

J Mol Biol, 1999

doi:10.1006/jmbi.1999.2642.

Protein-DNA interactions: A structural analysis.

Jones S, van Heyningen P, Berman HM, Thornton JM.

J Mol Biol, 1999

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, 1999

doi:10.1107/s0907444999002231.

Protein structural topology: Automated analysis and diagrammatic representation.

Westhead DR, Slidel TW, Flores TP, Thornton JM.

Protein Sci, 1999

doi:10.1110/ps.8.4.897.

Factors limiting the performance of prediction-based fold recognition methods.

de la Cruz X, Thornton JM.

Protein Sci, 1999

doi:10.1110/ps.8.4.750.

The Future of Bioinformatics

Thornton JM.

1998

doi:.

Pattern Search over the TOPS Protein Topology Database

Gilbert DR, Westhead DR, Hatton DC, Thornton JM.

Protein Data Bank Quarterly Newsletter, 1998

doi:.

Protein structure prediction.

Westhead DR, Thornton JM.

Curr Opin Biotechnol, 1998

doi:10.1016/s0958-1669(98)80012-8.

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, 1998

doi:10.1006/jmbi.1997.1621.

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, 1998

doi:10.1002/pro.5560070202.

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

J Mol Biol, 1998

doi:10.1006/jmbi.1997.1526.

An atlas of protein topology cartoons available on the World-Wide Web.

Westhead DR, Hatton DC, Thornton JM.

Trends Biochem Sci, 1998

doi:10.1016/s0968-0004(97)01161-4.

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).

Patel SU, Osborn R, Rees S, Thornton JM.

Biochemistry, 1998

doi:10.1021/bi971747d.

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, 1998

doi:10.1107/s0907444998007501.

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, 1998

doi:10.1107/s0907444998007318.

Iditis: protein structure database.

Gardner S, Thornton J.

Acta Crystallogr D Biol Crystallogr, 1998

doi:10.1107/s0907444998007112.

Contemporary approaches to protein structure classification.

Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM.

Bioessays, 1998

doi:10.1002/(sici)1521-1878(199811)20:11<884::aid-bies3>3.0.co;2-h.

Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.

Milburn D, Laskowski RA, Thornton JM.

Protein Eng, 1998

doi:10.1093/protein/11.10.855.

Determinants of strand register in antiparallel beta-sheets of proteins.

Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN.

Protein Sci, 1998

doi:10.1002/pro.5560071106.

Validation of protein models derived from experiment.

Laskowski RA, MacArthur MW, Thornton JM.

Curr Opin Struct Biol, 1998

doi:10.1016/s0959-440x(98)80156-5.

PQS: a protein quaternary structure file server.

Henrick K, Thornton JM.

Trends Biochem Sci, 1998

doi:10.1016/s0968-0004(98)01253-5.

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, 1998

doi:10.1023/a:1016085005275.

1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.

Bloch C, Patel SU, Baud F, Zvelebil MJ, Carr MD, Sadler PJ, Thornton JM.

Proteins, 1998

doi:10.1002/(sici)1097-0134(19980815)32:3<334::aid-prot9>3.0.co;2-h.

Protein folds and functions.

Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM.

Structure, 1998

doi:10.1016/s0969-2126(98)00089-6.

Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.

Hubbard SJ, Beynon RJ, Thornton JM.

Protein Eng, 1998

doi:10.1093/protein/11.5.349.

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, 1998

doi:10.1006/jmbi.1998.1764.

Computational Approaches to Protein Ligand Interactions: Protein-heme Complexes

Karmirantzou MI, Thornton JM.

1997

doi:.

Assessment of comparative modeling in CASP2.

Martin AC, MacArthur MW, Thornton JM.

Proteins, 1997

doi:10.1002/(sici)1097-0134(1997)1+<14::aid-prot4>3.3.co;2-f.

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, 1997

doi:10.1016/s0968-0004(97)01140-7.

Modelling protein unfolding: hen egg-white lysozyme.

Williams MA, Thornton JM, Goodfellow JM.

Protein Eng, 1997

doi:10.1093/protein/10.8.895.

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.

Luscombe NM, Laskowski RA, Thornton JM.

Nucleic Acids Res, 1997

doi:10.1093/nar/25.24.4940.

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, 1997

doi:10.1002/pro.5560061104.

Non-randomness in side-chain packing: the distribution of interplanar angles.

Mitchell JB, Laskowski RA, Thornton JM.

Proteins, 1997

doi:10.1002/(sici)1097-0134(199711)29:3<370::aid-prot10>3.0.co;2-k.

CATH--a hierarchic classification of protein domain structures.

Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM.

Structure, 1997

doi:10.1016/s0969-2126(97)00260-8.

Prediction of protein-protein interaction sites using patch analysis.

Jones S, Thornton JM.

J Mol Biol, 1997

doi:10.1006/jmbi.1997.1233.

Analysis of protein-protein interaction sites using surface patches.

Jones S, Thornton JM.

J Mol Biol, 1997

doi:10.1006/jmbi.1997.1234.

Structures of N-termini of helices in proteins.

Doig AJ, MacArthur MW, Stapley BJ, Thornton JM.

Protein Sci, 1997

doi:10.1002/pro.5560060117.

Molecular Recogntion by Proteins - Protein-Ligand Interactions from a Structural Perspective

Wallace AC, Laskowski RA, Singh J, Thornton JM.

1996

doi:.

Chirality in Protein Structure

Slidel TWF, Thornton JM.

1996

doi:.

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, 1996

doi:10.1007/bf00228148.

Deviations from planarity of the peptide bond in peptides and proteins.

MacArthur MW, Thornton JM.

J Mol Biol, 1996

doi:10.1006/jmbi.1996.0705.

Protein clefts in molecular recognition and function.

Laskowski RA, Luscombe NM, Swindells MB, Thornton JM.

Protein Sci, 1996

doi:10.1002/pro.5560051206.

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, 1996

doi:10.1111/j.1432-1033.1996.0352r.x.

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.

Martin AC, Thornton JM.

J Mol Biol, 1996

doi:10.1006/jmbi.1996.0617.

Protein recognition of adenylate: an example of a fuzzy recognition template.

Moodie SL, Mitchell JB, Thornton JM.

J Mol Biol, 1996

doi:10.1006/jmbi.1996.0591.

Antibody-antigen interactions: contact analysis and binding site topography.

MacCallum RM, Martin AC, Thornton JM.

J Mol Biol, 1996

doi:10.1006/jmbi.1996.0548.

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, 1996

doi:10.1002/(sici)1097-0134(199604)24:4<502::aid-prot9>3.0.co;2-f.

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, 1996

doi:10.1111/j.1399-3011.1996.tb01093.x.

Analysis of domain structural class using an automated class assignment protocol.

Michie AD, Orengo CA, Thornton JM.

J Mol Biol, 1996

doi:10.1006/jmbi.1996.0506.

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, 1996

doi:10.1002/pro.5560050603.

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, 1996

doi:10.1016/s0968-0004(96)10037-2.

Potential energy functions for threading.

Jones DT, Thornton JM.

Curr Opin Struct Biol, 1996

doi:10.1016/s0959-440x(96)80076-5.

PROMOTIF--a program to identify and analyze structural motifs in proteins.

Hutchinson EG, Thornton JM.

Protein Sci, 1996

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, 1996

doi:10.1016/0161-5890(95)00138-7.

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, 1996

doi:10.1006/jmbi.1996.0311.

Molecular recognition by proteins: protein-ligand interactions from a structural perspective.

Wallace AC, Laskowski RA, Singh J, Thornton JM.

Biochem Soc Trans, 1996

doi:10.1042/bst0240280.

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, 1996

doi:10.1006/jmbi.1996.0041.

Protein fold recognition by sequence threading: tools and assessment techniques.

Miller RT, Jones DT, Thornton JM.

FASEB J, 1996

doi:10.1096/fasebj.10.1.8566539.

Principles of protein-protein interactions.

Jones S, Thornton JM.

Proc Natl Acad Sci U S A, 1996

doi:10.1073/pnas.93.1.13.

Protein Engineering - Editorial Overview

Thornton JM, Berg JM.

1995

doi:.

Chirality in Proteins

Slidel TMW, Thornton JM.

1995

doi:.

Modelling the Interaction of Protein Side Chains

Mitchell JBO, Thornton JM, Price SL.

1995

doi:.

Software Tools for Protein Structure Analysis and Fold Classification

Michie AD, Hutchinson EG, Laskowski RA, Orengo CM, Thornton JM.

1995

doi:.

Protein Folds and Folding

Thornton JM, Jones DT, MacArthur M, Orengo CA, Swindells M.

FASEB J, 1995

doi:.

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, 1995

doi:.

Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.

Swindells MB, MacArthur MW, Thornton JM.

Nat Struct Biol, 1995

doi:10.1038/nsb0795-596.

Long loops in proteins.

Martin AC, Toda K, Stirk HJ, Thornton JM.

Protein Eng, 1995

doi:10.1093/protein/8.11.1093.

Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.

Jones DT, Miller RT, Thornton JM.

Proteins, 1995

doi:10.1002/prot.340230312.

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, 1995

doi:10.1002/pro.5560041003.

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, 1995

doi:10.1093/protein/8.3.217.

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.

Wallace AC, Laskowski RA, Thornton JM.

Protein Eng, 1995

doi:10.1093/protein/8.2.127.

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, 1995

doi:10.1098/rstb.1995.0047.

Protein-protein interactions: a review of protein dimer structures.

Jones S, Thornton JM.

Prog Biophys Mol Biol, 1995

doi:10.1016/0079-6107(94)00008-w.

Protein superfamilies and domain superfolds.

Orengo CA, Jones DT, Thornton JM.

Nature, 1994

doi:10.1038/372631a0.

Buried waters and internal cavities in monomeric proteins.

Williams MA, Goodfellow JM, Thornton JM.

Protein Sci, 1994

doi:10.1002/pro.5560030808.

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.

Hubbard SJ, Eisenmenger F, Thornton JM.

Protein Sci, 1994

doi:10.1002/pro.5560030505.

NMR and crystallography--complementary approaches to structure determination.

MacArthur MW, Driscoll PC, Thornton JM.

Trends Biotechnol, 1994

doi:10.1016/0167-7799(94)90074-4.

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, 1994

doi:10.1006/jmbi.1994.1370.

Satisfying hydrogen bonding potential in proteins.

McDonald IK, Thornton JM.

J Mol Biol, 1994

doi:10.1006/jmbi.1994.1334.

The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.

Stirk HJ, Thornton JM.

Protein Eng, 1994

doi:10.1093/protein/7.1.47.

An algorithm for automatically generating protein topology cartoons.

Flores TP, Moss DS, Thornton JM.

Protein Eng, 1994

doi:10.1093/protein/7.1.31.

A model recognition approach to the prediction of all-helical membrane protein structure and topology.

Jones DT, Taylor WR, Thornton JM.

Biochemistry, 1994

doi:10.1021/bi00176a037.

A mutation data matrix for transmembrane proteins.

Jones DT, Taylor WR, Thornton JM.

FEBS Lett, 1994

doi:10.1016/0014-5793(94)80429-x.

Knowledge-based validation of protein-structure coordinates derived by x-ray Cyrstallography and NMR-Spectroscopy

MacArthur MW, Laskowski RA, Thornton JM.

1994

doi:.

Evaluation of Protein Coordinate Data Sets

Laskowski RA, MacArthur MW, Thornton JM.

1994

doi:.

Protein Motifs and Folding Recognition

Thornton JM, Orengo CM, Jones DT, Taylor WR.

Biophys J, 1994

doi:.

A revised set of potentials for beta-turn formation in proteins.

Hutchinson EG, Thornton JM.

Protein Sci, 1994

doi:10.1002/pro.5560031206.

Alpha plus beta folds revisited: some favoured motifs.

Orengo CA, Thornton JM.

Structure, 1993

doi:10.1016/0969-2126(93)90026-d.

Peptide-protein interactions: an overview.

Zvelebil MJ, Thornton JM.

Q Rev Biophys, 1993

doi:10.1017/s0033583500002870.

Conformational analysis of protein structures derived from NMR data.

MacArthur MW, Thornton JM.

Proteins, 1993

doi:10.1002/prot.340170303.

Comparison of conformational characteristics in structurally similar protein pairs.

Flores TP, Orengo CA, Moss DS, Thornton JM.

Protein Sci, 1993

doi:10.1002/pro.5560021104.

Identification, classification, and analysis of beta-bulges in proteins.

Chan AW, Hutchinson EG, Harris D, Thornton JM.

Protein Sci, 1993

doi:10.1002/pro.5560021004.

A study of structural determinants in the interleukin-1 fold.

Swindells MB, Thornton JM.

Protein Eng, 1993

doi:10.1093/protein/6.7.711.

Protein fold recognition.

Jones D, Thornton J.

J Comput Aided Mol Des, 1993

doi:10.1007/bf02337560.

Identification and classification of protein fold families.

Orengo CA, Flores TP, Taylor WR, Thornton JM.

Protein Eng, 1993

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, 1993

doi:10.1093/protein/6.5.461.

Main-chain bond lengths and bond angles in protein structures.

Laskowski RA, Moss DS, Thornton JM.

J Mol Biol, 1993

doi:10.1006/jmbi.1993.1351.

Atomic environments of arginine side chains in proteins.

Nandi CL, Singh J, Thornton JM.

Protein Eng, 1993

doi:10.1093/protein/6.3.247.

The Greek key motif: extraction, classification and analysis.

Hutchinson EG, Thornton JM.

Protein Eng, 1993

doi:10.1093/protein/6.3.233.

A study into the effects of protein binding on nucleotide conformation.

Moodie SL, Thornton JM.

Nucleic Acids Res, 1993

doi:10.1093/nar/21.6.1369.

Molecular modelling and epitope prediction of gp29 from lymphatic filariae.

Zvelebil MJ, Tang L, Cookson E, Selkirk ME, Thornton JM.

Mol Biochem Parasitol, 1993

doi:10.1016/0166-6851(93)90098-i.

Recurrence of a binding motif?

Swindells MB, Orengo CA, Jones DT, Pearl LH, Thornton JM.

Nature, 1993

doi:10.1038/362299a0.

Accommodating sequence changes in beta-hairpins in proteins.

Sibanda BL, Thornton JM.

J Mol Biol, 1993

doi:10.1006/jmbi.1993.1044.

Modelling of related protein structures

Thornton JM, Swindells MB.

1993

doi:.

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.

1993

doi:.

Database Analysis for Protein Engineering

Thornton JM, Gardner SP.

1993

doi:.

Recurrence of a Binding Motif

Swindells MJ, Orengo CA, Jones DT, Pearl LH, Thornton JM.

Nature, 1993

doi:.

Shared Structural Motif in Proteins - Reply

Swindells MJ, Orengo CA, Jones DT, Pearl LH, Thornton JM.

Nature, 1993

doi:10.1038/365021b0.

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, 1993

doi:.

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, 1993

doi:.

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, 1993

doi:.

Amino Aromatic Interactions

Mitchell JBO, Nandi CL, Ali S, McDonald JK, Thornton JM, Price SL, Singh J.

Nature, 1993

doi:10.1038/366413a0.

Progress Towards Recognizing Protein Folds from Amino-Acid-Sequence

Jones DT, Orengo C, Taylor WR, Thornton JM.

Protein Eng, 1993

doi:.

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, 1993

doi:.

PROCHECK: a program to check the stereochemical quality of protein structures.

Laskowski RA, MacArthur MW, Moss DS, Thornton JM.

J Appl Crystallogr, 1993

doi:10.1107/s0021889892009944.

Recurring structural motifs in proteins with different functions.

Orengo CA, Flores TP, Jones DT, Taylor WR, Thornton JM.

Curr Biol, 1993

doi:10.1016/0960-9822(93)90254-l.

Substrate recognition by proteinases.

Hubbard SJ, Thornton JM, Campbell SF.

Faraday Discuss, 1992

doi:10.1039/fd9929300013.

A topological model for hepatitis B surface antigen.

Stirk HJ, Thornton JM, Howard CR.

Intervirology, 1992

doi:10.1159/000150244.

Depicting topology and handedness in jellyroll structures.

Stirk HJ, Woolfson DN, Hutchinson EG, Thornton JM.

FEBS Lett, 1992

doi:10.1016/0014-5793(92)81036-l.

The rapid generation of mutation data matrices from protein sequences.

Jones DT, Taylor WR, Thornton JM.

Comput Appl Biosci, 1992

doi:10.1093/bioinformatics/8.3.275.

Towards an understanding of the arginine-aspartate interaction.

Mitchell JB, Thornton JM, Singh J, Price SL.

J Mol Biol, 1992

doi:10.1016/0022-2836(92)90137-9.

A new approach to protein fold recognition.

Jones DT, Taylor WR, Thornton JM.

Nature, 1992

doi:10.1038/358086a0.

Stereochemical quality of protein structure coordinates.

Morris AL, MacArthur MW, Hutchinson EG, Thornton JM.

Proteins, 1992

doi:10.1002/prot.340120407.

Secondary and Supersecondary Motifs in Protein Structures

Thornton JM, Sibanda BL, Wilmott CM, Singh J.

1992

doi:.

Protein Structures: The End Point of the Folding Pathway

Thornton JM.

1992

doi:.

Lessons in Analysing Protein Structures

Thornton JM.

1992

doi:.

Atlas of Protein Side-Chain Interactions

Singh J, Thornton JM.

1992

doi:.

Towards an understanding how side-chains pack in proteins

Singh J, Nandi LC, Thornton JM.

1992

doi:.

A novel method for the modelling of peptide ligands to their receptors.

Singh J, Saldanha J, Thornton JM.

Protein Eng, 1991

doi:10.1093/protein/4.3.251.

Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors.

Hubbard SJ, Campbell SF, Thornton JM.

J Mol Biol, 1991

doi:10.1016/0022-2836(91)90027-4.

Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins.

Hunter CA, Singh J, Thornton JM.

J Mol Biol, 1991

doi:10.1016/0022-2836(91)90271-7.

Influence of proline residues on protein conformation.

MacArthur MW, Thornton JM.

J Mol Biol, 1991

doi:10.1016/0022-2836(91)90721-h.

An extension of secondary structure prediction towards the prediction of tertiary structure.

Garratt RC, Thornton JM, Taylor WR.

FEBS Lett, 1991

doi:10.1016/0014-5793(91)80223-p.

Conformation of beta hairpins in protein structures: classification and diversity in homologous structures.

Sibanda BL, Thornton JM.

Methods Enzymol, 1991

doi:10.1016/0076-6879(91)02007-v.

Protein Structure Database

Thornton JM, Gardner SP, Hutchinson EG.

1991

doi:.

Modelling Antibody Combining Sites: A Review

Thornton JM.

1991

doi:.

Protein Structure

Thornton JM, Barlow DJ.

1991

doi:.

Protein Structure, Prediction and Design

Thornton JM.

1991

doi:.

Modelling by Homology

Swindells MB, Thornton JM.

1991

doi:.

Trypanothine Metabolism as a Target for Drug Design: Molecular Modelling of Trypanothine Reductase in Biochemical Protozoology

Smith K, Mills A, Thornton JM, Fairlamb AH.

1991

doi:.

Structural Patterns in Globular Proteins

Hutchinson EG, Morris AL, Thornton JM.

1991

doi:.

The Iditis Relational Database of Protein Structure

Gardner SP, Thornton JM.

1991

doi:.

Modelling antibody combining sites: a review.

Thornton JM.

Ciba Found Symp, 1991

doi:10.1002/9780470514108.ch5.

Structure prediction and modelling.

Swindells MB, Thornton JM.

Curr Opin Biotechnol, 1991

doi:10.1016/0958-1669(91)90074-f.

Protein structure. Prediction of progress at last.

Thornton JM, Flores TP, Jones DT, Swindells MB.

Nature, 1991

doi:10.1038/354105a0.

Analysis of protein main-chain solvation as a function of secondary structure.

Thanki N, Umrania Y, Thornton JM, Goodfellow JM.

J Mol Biol, 1991

doi:10.1016/0022-2836(91)80080-e.

HERA--a program to draw schematic diagrams of protein secondary structures.

Hutchinson EG, Thornton JM.

Proteins, 1990

doi:10.1002/prot.340080303.

Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins.

Thanki N, Thornton JM, Goodfellow JM.

Protein Eng, 1990

doi:10.1093/protein/3.6.495.

Beta-turns and their distortions: a proposed new nomenclature.

Wilmot CM, Thornton JM.

Protein Eng, 1990

doi:10.1093/protein/3.6.479.

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups.

Singh J, Thornton JM.

J Mol Biol, 1990

doi:10.1016/0022-2836(90)90268-q.

Antibody modelling. Tackling a loopy problem.

Thornton JM.

Nature, 1990

doi:10.1038/343411a0.

Antibody Modelling - Tackling a Loopy Problem

Thornton JM.

Nature, 1990

doi:pmid: 2300188.

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, 1989

doi:10.1093/protein/3.1.23.

Protein motifs and data-base searching.

Thornton JM, Gardner SP.

Trends Biochem Sci, 1989

doi:10.1016/0968-0004(89)90069-8.

Rebuilding flavodoxin from C alpha coordinates: a test study.

Reid LS, Thornton JM.

Proteins, 1989

doi:10.1002/prot.340050212.

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, 1989

doi:10.1016/0022-2836(89)90583-4.

Structure Prediction

Thornton JM, Taylor WR.

1989

doi:.

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, 1989

doi:.

Preliminary Analysis of Water Molecule Disitributions in Proteins

Goodfellow JM, Thanki N, Thornton JM.

Mol Simul, 1989

doi:10.1080/08927028908034626.

Protein-protein recognition via side-chain interactions.

Thornton JM, Singh J, Campbell S, Blundell TL.

Biochem Soc Trans, 1988

doi:10.1042/bst0160927.