The rapid generation of mutation data matrices from protein sequences. - David T. Jones; William R. Taylor; Janet M. Thornton (Comput. Appl. Biosci., 1992)

Protein fold recognition. - David T. Jones; Janet M. Thornton (J. Comput. Aided Mol. Des., 1993)

[Invited Lecture] Protein Folds and Functions. - Janet M. Thornton; Andrew C. R. Martin; Christine A. Orengo; Duncan Milburn; Roman A. Laskowski (German Conference on Bioinformatics, 1998)

Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania. - Fabio Zuccotto; Andrew C. R. Martin; Roman A. Laskowski; Janet M. Thornton; Ian H. Gilbert (J. Comput. Aided Mol. Des., 1998)

Motif-based searching in TOPS protein topology databases. - David R. Gilbert; David R. Westhead; Nozomi Nagano; Janet M. Thornton (Bioinform., 1999)

BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data. - John B. O. Mitchell; Roman A. Laskowski; Alexander Alex; Mark J. Forster; Janet M. Thornton (J. Comput. Chem., 1999)

BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential. - John B. O. Mitchell; Roman A. Laskowski; Alexander Alex; Janet M. Thornton (J. Comput. Chem., 1999)

The CATH Database provides insights into protein structure/function relationships. - Christine A. Orengo; Frances M. G. Pearl; James E. Bray; Annabel E. Todd; A. C. Martin; Loredana Lo Conte; Janet M. Thornton (Nucleic Acids Res., 1999)

Une technique déclarative pour filtrer des motifs topologiques de protéines. - David R. Gilbert; David R. Westhead; Janet M. Thornton; Karine Yvon (JFPLC, 2000)

Assigning genomic sequences to CATH. - Frances M. G. Pearl; David A. Lee; James E. Bray; Ian Sillitoe; Annabel E. Todd; Andrew P. Harrison; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2000)

Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes. - Irene Nobeli; John B. O. Mitchell; Alexander Alex; Janet M. Thornton (J. Comput. Chem., 2001)

Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level. - Nicholas M. Luscombe; Roman A. Laskowski; Janet M. Thornton (Nucleic Acids Res., 2001)

A rapid classification protocol for the CATH Domain Database to support structural genomics. - Frances M. G. Pearl; Nigel J. Martin 001; James E. Bray; Daniel W. A. Buchan; Andrew P. Harrison; David A. Lee; Gabrielle A. Reeves; Adrian J. Shepherd; Ian Sillitoe; Annabel E. Todd; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2001)

A Computer System to Perform Structure Comparison using Representations of Protein Structure. - David R. Gilbert; David R. Westhead; Juris Viksna; Janet M. Thornton (Comput. Chem., 2002)

The proteome and the metabolome. - Janet M. Thornton (ECCB, 2003)

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. - Jonathan A. Barker; Janet M. Thornton (Bioinform., 2003)

Recognizing the fold of a protein structure. - Andrew P. Harrison; Frances M. G. Pearl; Ian Sillitoe; Tim Slidel; Richard Mott; Janet M. Thornton; Christine A. Orengo (Bioinform., 2003)

Gene3D: structural assignments for the biologist and bioinformaticist alike. - Daniel W. A. Buchan; Stuart C. G. Rison; James E. Bray; David A. Lee; Frances M. G. Pearl; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2003)

The CATH database: an extended protein family resource for structural and functional genomics. - Frances M. G. Pearl; C. F. Bennett; James E. Bray; Andrew P. Harrison; Nigel J. Martin 001; Adrian J. Shepherd; Ian Sillitoe; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2003)

Software Engineering Challenges in Bioinformatics. - Jonathan A. Barker; Janet M. Thornton (ICSE, 2004)

SCOPEC: a database of protein catalytic domains. - Richard A. George; Ruth V. Spriggs; Janet M. Thornton; Bissan Al-Lazikani; Mark B. Swindells (ISMB/ECCB (Supplement of Bioinformatics), 2004)

ISMB/ECCB 2004. - Janet M. Thornton; David R. Gilbert; Catherine Brooksbank (ISMB/ECCB (Supplement of Bioinformatics), 2004)

ISMB/ECCB 2004 Organization. - Janet M. Thornton; David R. Gilbert; Catherine Brooksbank (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Microeconomic Principles Explain an Optimal Genome Size in Bacteria. - Juan Garcia Ranea; Alastair Grant; Janet M. Thornton; Christine A. Orengo (Spanish Bioinformatics Conference, 2004)

A practical and robust sequence search strategy for structural genomics target selection. - James E. Bray; Russell L. Marsden; Stuart C. G. Rison; Alexei Savchenko; Aled M. Edwards; Janet M. Thornton; Christine A. Orengo (Bioinform., 2004)

An examination of the conservation of surface patch polarity for proteins. - Hugh P. Shanahan; Janet M. Thornton (Bioinform., 2004)

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. - Craig T. Porter; Gail J. Bartlett; Janet M. Thornton (Nucleic Acids Res., 2004)

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif. - Carles Ferrer-Costa; Hugh P. Shanahan; Susan Jones; Janet M. Thornton (Bioinform., 2005)

MACiE: a database of enzyme reaction mechanisms. - Gemma L. Holliday; Gail J. Bartlett; Daniel E. Almonacid; Noel M. O'Boyle; Peter Murray-Rust; Janet M. Thornton; John B. O. Mitchell (Bioinform., 2005)

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. - Richard J. Morris; Rafael Najmanovich; Abdullah Kahraman; Janet M. Thornton (Bioinform., 2005)

Living longer by dieting: analysis of transcriptional response after caloric restriction. - Nicola D. Kerrison; Colin Selman; Steven J. Lingard; Janet M. Thornton; Linda Partridge; Dominic J. Withers (BMC Bioinform., 2005)

The European Bioinformatics Institute's data resources: towards systems biology. - Catherine Brooksbank; Graham Cameron; Janet M. Thornton (Nucleic Acids Res., 2005)

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. - Roman A. Laskowski; Victor V. Chistyakov; Janet M. Thornton (Nucleic Acids Res., 2005)

ProFunc: a server for predicting protein function from 3D structure. - Roman A. Laskowski; James D. Watson; Janet M. Thornton (Nucleic Acids Res., 2005)

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. - Frances M. G. Pearl; Annabel E. Todd; Ian Sillitoe; Mark Dibley; Oliver Redfern; Tony E. Lewis; Christopher Bennett; Russell L. Marsden; Alastair Grant; David A. Lee; Adrian Akpor; Michael Maibaum; et al. (Nucleic Acids Res., 2005)

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. - Rafael Najmanovich; Abdellah Allali-Hassani; Richard J. Morris; Ludmila Dombrovsky; Patricia W. Pan; Masoud Vedadi; Alexander N. Plotnikov; Aled M. Edwards; Cheryl H. Arrowsmith; Janet M. Thornton (Bioinform., 2007)

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands. - Abdullah Kahraman; Richard J. Morris; Roman A. Laskowski; Janet M. Thornton (BMC Bioinform., 2007)

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. - Lesley H. Greene; Tony E. Lewis; Sarah Addou; Alison L. Cuff; Timothy Dallman; Mark Dibley; Oliver Redfern; Frances M. G. Pearl; Rekha Nambudiry; Adam James Reid; Ian Sillitoe; Corin Yeats; et al. (Nucleic Acids Res., 2007)

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. - Gemma L. Holliday; Daniel E. Almonacid; Gail J. Bartlett; Noel M. O'Boyle; James W. Torrance; Peter Murray-Rust; John B. O. Mitchell; Janet M. Thornton (Nucleic Acids Res., 2007)

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data. - Tom C. Freeman; Leon Goldovsky; Markus Brosch; Stijn van Dongen; Pierre Mazière; Russell J. Grocock; Shiri Freilich; Janet M. Thornton; Anton J. Enright (PLoS Comput. Biol., 2007)

Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network. - Jonathan J. Ward; Janet M. Thornton (PLoS Comput. Biol., 2007)

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. - Rafael Najmanovich; Natalja Kurbatova; Janet M. Thornton (ECCB, 2008)

The Protein Feature Ontology: a tool for the unification of protein feature annotations. - Gabrielle A. Reeves; Karen Eilbeck; Michele Magrane; Claire O'Donovan; Luisa Montecchi-Palazzi; Midori A. Harris; Sandra E. Orchard; Rafael C. Jiménez; Andreas Prlic; Tim J. P. Hubbard; Henning Hermjakob; Janet M. Thornton (Bioinform., 2008)

PROCOGNATE: a cognate ligand domain mapping for enzymes. - Matthew Bashton; Irene Nobeli; Janet M. Thornton (Nucleic Acids Res., 2008)

ELIXIR - A European Infrastructure for Biological Information: Challenges and Progress. - Janet M. Thornton (GI Jahrestagung, 2009)

Metal-MACiE: a database of metals involved in biological catalysis. - Claudia Andreini; Ivano Bertini; Gabriele Cavallaro; Gemma L. Holliday; Janet M. Thornton (Bioinform., 2009)

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins. - Romina Oliva; Janet M. Thornton; Marialuisa Pellegrini-Calace (Bioinform., 2009)

WSsas: a web service for the annotation of functional residues through structural homologues. - David Talavera; Roman A. Laskowski; Janet M. Thornton (Bioinform., 2009)

Small Molecule Subgraph Detector (SMSD) toolkit. - Syed Asad Rahman; Matthew Bashton; Gemma L. Holliday; Rainer Schrader; Janet M. Thornton (J. Cheminformatics, 2009)

Mapping Human Metabolic Pathways in the Small Molecule Chemical Space. - Antonio Macchiarulo; Janet M. Thornton; Irene Nobeli (J. Chem. Inf. Model., 2009)

The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies. - Alison L. Cuff; Ian Sillitoe; Tony E. Lewis; Oliver Redfern; Richard Garratt; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2009)

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. - John A. Capra; Roman A. Laskowski; Janet M. Thornton; Mona Singh 001; Thomas A. Funkhouser (PLoS Comput. Biol., 2009)

PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure. - Marialuisa Pellegrini-Calace; Tim Maiwald; Janet M. Thornton (PLoS Comput. Biol., 2009)

The CoFactor database: organic cofactors in enzyme catalysis. - Julia D. Fischer; Gemma L. Holliday; Janet M. Thornton (Bioinform., 2010)

The European Bioinformatics Institute's data resources. - Catherine Brooksbank; Graham Cameron; Janet M. Thornton (Nucleic Acids Res., 2010)

Extending CATH: increasing coverage of the protein structure universe and linking structure with function. - Alison L. Cuff; Ian Sillitoe; Tony E. Lewis; Andrew B. Clegg; Robert Rentzsch; Nicholas Furnham; Marialuisa Pellegrini-Calace; David T. Jones; Janet M. Thornton; Christine A. Orengo (Nucleic Acids Res., 2011)

Delivering ICT infrastructure for biomedical research. - Tommi H. Nyrönen; Jarno Laitinen; Olli Tourunen; Danny Sternkopf; Risto Laurikainen; Per Öster; Pekka T. Lehtovuori; Timo A. Miettinen; Tomi Simonen; Teemu Perheentupa; Imre Vastrik; Olli-P. Kallioniemi; et al. (WICSA/ECSA Companion Volume, 2012)

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. - Nicholas Furnham; Ian Sillitoe; Gemma L. Holliday; Alison L. Cuff; Syed Asad Rahman; Roman A. Laskowski; Christine A. Orengo; Janet M. Thornton (Nucleic Acids Res., 2012)

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies. - Nicholas Furnham; Ian Sillitoe; Gemma L. Holliday; Alison L. Cuff; Roman A. Laskowski; Christine A. Orengo; Janet M. Thornton (PLoS Comput. Biol., 2012)

The EBI enzyme portal. - Rafael Alcántara; Joseph Onwubiko; Hong Cao; Paula de Matos; Jennifer A. Cham; Julius O. B. Jacobsen; Gemma L. Holliday; Julia D. Fischer; Syed Asad Rahman; Bijay Jassal; Mickael Goujon; Francis Rowland; et al. (Nucleic Acids Res., 2013)

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. - Ian Sillitoe; Alison L. Cuff; Benoit H. Dessailly; Natalie L. Dawson; Nicholas Furnham; David A. Lee; Jonathan G. Lees; Tony E. Lewis; Romain A. Studer; Robert Rentzsch; Corin Yeats; Janet M. Thornton; et al. (Nucleic Acids Res., 2013)

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset. - Tjaart A. P. de Beer; Roman A. Laskowski; Sarah L. Parks; Botond Sipos; Nick Goldman; Janet M. Thornton (PLoS Comput. Biol., 2013)

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing. - Irene Papatheodorou; Rudolfs Petrovs; Janet M. Thornton (Bioinform., 2014)

PDBsum additions. - Tjaart A. P. de Beer; Karel Berka; Janet M. Thornton; Roman A. Laskowski (Nucleic Acids Res., 2014)

The European Bioinformatics Institute's data resources 2014. - Catherine Brooksbank; Mary Todd Bergman; Rolf Apweiler; Ewan Birney; Janet M. Thornton (Nucleic Acids Res., 2014)

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. - Nicholas Furnham; Gemma L. Holliday; Tjaart A. P. de Beer; Julius O. B. Jacobsen; William R. Pearson; Janet M. Thornton (Nucleic Acids Res., 2014)

SurvCurv database and online survival analysis platform update. - Matthias Ziehm; Dobril K. Ivanov; Aditi Bhat; Linda Partridge; Janet M. Thornton (Bioinform., 2015)

CATH: comprehensive structural and functional annotations for genome sequences. - Ian Sillitoe; Tony E. Lewis; Alison L. Cuff; Sayoni Das; Paul Ashford; Natalie L. Dawson; Nicholas Furnham; Roman A. Laskowski; David A. Lee; Jonathan G. Lees; Sonja Lehtinen; Romain A. Studer; et al. (Nucleic Acids Res., 2015)

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. - Nidhi Tyagi; Edward J. Farnell; Colin M. Fitzsimmons; Stephanie Ryan; Edridah M. Tukahebwa; Rick M. Maizels; David W. Dunne; Janet M. Thornton; Nicholas Furnham (PLoS Comput. Biol., 2015)

Reaction Decoder Tool (RDT): extracting features from chemical reactions. - Syed Asad Rahman; Gilliean Torrance; Lorenzo Baldacci; Sergio Martínez Cuesta; Franz Fenninger; Nimish Gopal; Saket Choudhary; John W. May; Gemma L. Holliday; Christoph Steinbeck; Janet M. Thornton (Bioinform., 2016)

Transform-MinER: transforming molecules in enzyme reactions. - Jonathan D. Tyzack; António J. M. Ribeiro; Neera Borkakoti; Janet M. Thornton (Bioinform., 2018)

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. - António J. M. Ribeiro; Gemma L. Holliday; Nicholas Furnham; Jonathan D. Tyzack; Katherine Ferris; Janet M. Thornton (Nucleic Acids Res., 2018)

Finding enzyme cofactors in Protein Data Bank. - Abhik Mukhopadhyay; Neera Borkakoti; Lukás Pravda; Jonathan D. Tyzack; Janet M. Thornton; Sameer Velankar (Bioinform., 2019)

VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. - James D. Stephenson; Roman A. Laskowski; Andrew Nightingale; Matthew E. Hurles; Janet M. Thornton (Bioinform., 2019)

CATH: expanding the horizons of structure-based functional annotations for genome sequences. - Ian Sillitoe; Natalie L. Dawson; Tony E. Lewis; Sayoni Das; Jonathan G. Lees; Paul Ashford; Adeyelu Tolulope; Harry M. Scholes; Ilya Senatorov; Andra Bujan; Fatima Ceballos Rodriguez-Conde; Benjamin Dowling; et al. (Nucleic Acids Res., 2019)

Using the drug-protein interactome to identify anti-ageing compounds for humans. - Matías Fuentealba; Handan Melike Dönertas; Rhianna Williams; Johnathan Labbadia; Janet M. Thornton; Linda Partridge (PLoS Comput. Biol., 2019)

GRaSP: a graph-based residue neighborhood strategy to predict binding sites. - Charles Abreu Santana; Sabrina de Azevedo Silveira; João P. A. Moraes; Sandro C. Izidoro; Raquel Cardoso de Melo Minardi; António J. M. Ribeiro; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton (Bioinform., 2020)

An automated protocol for modelling peptide substrates to proteases. - Rodrigo Ochoa; Mikhail D. Magnitov; Roman A. Laskowski; Pilar Cossio; Janet M. Thornton (BMC Bioinform., 2020)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

Srinivasan (1962-2021) in Bioinformatics and beyond. - M. Michael Gromiha; Christine A. Orengo; Ramanathan Sowdhamini; Janet M. Thornton (Bioinform., 2022)

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. - Charles Abreu Santana; Sandro C. Izidoro; Raquel Cardoso de Melo Minardi; Jonathan D. Tyzack; António J. M. Ribeiro; Douglas E. V. Pires; Janet M. Thornton; Sabrina de Azevedo Silveira (Nucleic Acids Res., 2022)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. - Ondrej Vavra; Jonathan D. Tyzack; Farzan Haddadi; Jan Stourac; Jirí Damborský; Stanislav Mazurenko; Janet M. Thornton; David Bednar (J. Cheminformatics, 2024)