J. Thornton

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CATH--a hierarchic classification of protein domain structures.

David C. Jones, C. Orengo, A. Michie, 1997, Structure.

Prediction of strand pairing in antiparallel and parallel β‐sheets using information theory

J. Thornton, R. E. Steward, 2002, Proteins.

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

J. Thornton, S. Teichmann, S. C. Rison, 2002, Journal of molecular biology.

Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin‐43, an α‐helical protein with over 50% sequence identity to an all‐β protein

David T. Jones, David C. Jones, J. Thornton, 1996 .

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.

D. T. Jones, J. Thornton, C. Moody, 1996, Proteins.

Using a neural network and spatial clustering to predict the location of active sites in enzymes.

Gail J. Bartlett, J. Thornton, Alex Gutteridge, 2003, Journal of molecular biology.

Protein clefts in molecular recognition and function.

M. Swindells, J. Thornton, N. Luscombe, 1996, Protein science : a publication of the Protein Society.

Analysis of catalytic residues in enzyme active sites.

Gail J. Bartlett, J. Thornton, C. T. Porter, 2002, Journal of molecular biology.

PROMOTIF—A program to identify and analyze structural motifs in proteins

J. Thornton, E. Hutchinson, 1996, Protein science : a publication of the Protein Society.

Protein superfamilles and domain superfolds

David T. Jones, C. Orengo, J. Thornton, 1994, Nature.

Ion-pairs in proteins.

J. Thornton, D. Barlow, Janet M. Thornton, 1983, Journal of molecular biology.

Conformational analysis of protein structures derived from NMR data

J. Thornton, M. W. Macarthur, M. W. MacArthur, 1993, Proteins.

Quantifying the similarities within fold space.

Frances M. G. Pearl, J. Thornton, R. Mott, 2002, Journal of molecular biology.

From structure to function: Approaches and limitations

Annabel E. Todd, C. Orengo, J. Thornton, 2000, Nature Structural Biology.

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

Annabel E. Todd, C. Orengo, J. Thornton, 2001, Journal of molecular biology.

The European dimension for the mouse genome mutagenesis program

Steve D. M. Brown, J. Thornton, A. Ballabio, 2004 .

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

J. Thornton, N. Borkakoti, A. C. Wallace, 1997, Protein science : a publication of the Protein Society.

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

J. Thornton, R. Laskowski, M. W. Macarthur, 1993 .

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.

C. Orengo, J. Thornton, N. Nagano, 2002, Journal of molecular biology.

Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.

Gail J. Bartlett, James W. Torrance, J. Thornton, 2005, Journal of molecular biology.

Predicting protein function from sequence and structural data.

J. Thornton, R. Laskowski, J. Watson, 2005, Current opinion in structural biology.

Protein motifs and data-base searching.

J. Thornton, S. Gardner, 1989, Trends in biochemical sciences.

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

Russell L. Marsden, C. Orengo, J. Thornton, 2005, Journal of molecular biology.

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.

Frances M. G. Pearl, Annabel E. Todd, J. Thornton, 2000, Protein engineering.

Prediction of protein-protein interaction sites using patch analysis.

S. Jones, J. Thornton, 1997, Journal of molecular biology.

From protein structure to function.

C. Orengo, J. Thornton, A. Todd, 1999, Current opinion in structural biology.

Evolution of protein superfamilies and bacterial genome size.

Daniel W. A. Buchan, C. Orengo, J. Thornton, 2004, Journal of molecular biology.

Assessment of comparative modeling in CASP2

Andrew C. R. Martin, J. Thornton, M. W. Macarthur, 1997, Proteins.

Potential energy functions for threading.

David C. Jones, D. T. Jones, J. Thornton, 1996, Current opinion in structural biology.

Conformational changes observed in enzyme crystal structures upon substrate binding.

J. Thornton, Alex Gutteridge, 2005, Journal of molecular biology.

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

J. Thornton, C. T. Porter, N. Nagano, 2001 .

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

J. Thornton, C. T. Porter, N. Nagano, 2001, Protein engineering.

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.

C. Chothia, J. Thornton, S. Teichmann, 2001, Journal of molecular biology.

AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR

J. Thornton, R. Laskowski, M. W. Macarthur, 1996, Journal of biomolecular NMR.

The CATH domain structure database.

Frances M. G. Pearl, C. Orengo, J. Thornton, 2005, Methods of biochemical analysis.

Protein structural topology: Automated analysis and diagrammatic representation

T. P. Flores, J. Thornton, D. Westhead, 2008, Protein science : a publication of the Protein Society.

PQS: a protein quaternary structure file server.

J. Thornton, K. Henrick, 1998, Trends in biochemical sciences.

Identification, classification, and analysis of beta‐bulges in proteins

J. Thornton, E. Hutchinson, A. W. Chan, 1993, Protein science : a publication of the Protein Society.

Analysis of protein-protein interaction sites using surface patches.

S. Jones, J. Thornton, 1997, Journal of molecular biology.

A method for localizing ligand binding pockets in protein structures

J. Thornton, R. Laskowski, F. Glaser, 2005, Proteins.

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

M. Swindells, J. Thornton, M. W. Macarthur, 1995, Nature structural biology.

Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures

M. Swindells, J. Thornton, M. W. Macarthur, 1995, Nature Structural Biology.

Influence of proline residues on protein conformation.

J. Thornton, M. W. Macarthur, M. W. MacArthur, 1991, Journal of molecular biology.

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

J. Thornton, C. Wilmot, 1990, Protein engineering.

Effective function annotation through catalytic residue conservation.

Gail J. Bartlett, R. A. George, M. Swindells, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Bioinformatics: Genes, Proteins and Computers

David T. Jones, C. Orengo, J. Thornton, 2007 .

Protein fold recognition

Janet M. Thornton, David T. Jones, David T. Jones, 1993, J. Comput. Aided Mol. Des..

Satisfying hydrogen bonding potential in proteins.

J. Thornton, I. McDonald, Janet M. Thornton, 1994, Journal of molecular biology.

Protein-RNA interactions: a structural analysis.

S. Jones, J. Thornton, N. Luscombe, 2001, Nucleic acids research.

Protein–protein interfaces: Analysis of amino acid conservation in homodimers

J. Thornton, W. S. Valdar, William S. J. Valdar, 2001, Proteins.

Searching for functional sites in protein structures.

J. Thornton, Susan Jones, 2004, Current opinion in chemical biology.

Plasticity of enzyme active sites.

C. Orengo, J. Thornton, A. Todd, 2002, Trends in biochemical sciences.

Buried waters and internal cavities in monomeric proteins

J. Thornton, Mark A. Williams, J. Goodfellow, 1994, Protein science : a publication of the Protein Society.

Identification and classification of protein fold families.

T. P. Flores, C. Orengo, J. Thornton, 1993, Protein engineering.

On the conformation of proteins: The handedness of the β-strand-α-helix-β-strand unit

M. Sternberg, J. Thornton, 1976 .

Continuous and discontinuous protein antigenic determinants

J. Thornton, D. Barlow, M. S. Edwards, 1986, Nature.

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

Andrew J. Martin, J. Thornton, R. MacCallum, 1996, Journal of molecular biology.

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

Janet M. Thornton, Craig T. Porter, Gail J. Bartlett, 2004, Nucleic Acids Res..

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

J. Thornton, M. W. Macarthur, M. W. MacArthur, 1996, Journal of molecular biology.

Stereochemical quality of protein structure coordinates

J. Thornton, E. Hutchinson, M. W. Macarthur, 1992, Proteins.

The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains.

J. Thornton, I. McDonald, 1995, Protein engineering.

An overview of the structures of protein-DNA complexes

J. Thornton, N. Luscombe, H. Berman, 2000, Genome Biology.

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

Andrew J. Martin, J. Thornton, A. C. Martin, 1996, Journal of molecular biology.

Computational biology for ageing

J. Thornton, I. Papatheodorou, D. Wieser, 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

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

S. Jones, J. Thornton, A. Marin, 2000, Protein engineering.

Determinants of strand register in antiparallel β‐sheets of proteins

J. Thornton, E. Hutchinson, R. Sessions, 1998, Protein science : a publication of the Protein Society.

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

J. Thornton, I. Nooren, Irene M.A. Nooren, 2003, Journal of molecular biology.

A revised set of potentials for β‐turn formation in proteins

J. Thornton, E. Hutchinson, 1994 .

The structural basis of allosteric regulation in proteins

J. Thornton, R. Laskowski, F. Gerick, 2009, FEBS letters.

Molecular basis of inherited diseases: a structural perspective.

J. Thornton, R. E. Steward, R. Laskowski, 2003, Trends in genetics : TIG.

Integrating mutation data and structural analysis of the TP53 tumor‐suppressor protein

Alison L. Cuff, J. Thornton, M. Olivier, 2002, Human mutation.

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

Janet M Thornton, Nicholas M Luscombe, J. Thornton, 2002, Journal of molecular biology.

Protein-DNA interactions: A structural analysis.

H M Berman, J M Thornton, S. Jones, 1999, Journal of molecular biology.

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

J M Thornton, S. Jones, J. Thornton, 1995, Progress in biophysics and molecular biology.

Discriminating between homodimeric and monomeric proteins in the crystalline state

J. Thornton, K. Henrick, H. Ponstingl, 2000, Proteins.

Morphological aspects of oligomeric protein structures.

Denise Gorse, Janet M Thornton, J. Thornton, 2005, Progress in biophysics and molecular biology.

Principles of protein-protein interactions.

S. Jones, J. Thornton, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Diversity of protein–protein interactions

J. Thornton, I. Nooren, Irene M.A. Nooren, 2003, The EMBO journal.

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

Rafael Najmanovich, Natalja Kurbatova, Janet Thornton, 2008 .

Three-dimensional structure analysis of PROSITE patterns.

J M Thornton, J. Thornton, A. Kasuya, 1999, Journal of molecular biology.

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

Janet M Thornton, Irene Nobeli, Jonathan A. Barker, 2003, Nucleic acids research.

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

J M Thornton, J. Thornton, H. Shanahan, 2005, Biopolymers.

Automatic inference of protein quaternary structure from crystals

Janet M. Thornton, J. Thornton, H. Ponstingl, 2003 .

The Hans Neurath Award lecture of The Protein Society: Proteins—A testament to physics, chemistry, and evolution

J. Thornton, 2001, Protein science : a publication of the Protein Society.

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

J M Thornton, J. Thornton, Juswinder Singh, 1990, Journal of molecular biology.

The interaction between phenylalanine rings in proteins

Janet M. Thornton, Juswinder Singh, J. Thornton, 1985 .

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

J M Thornton, J. Thornton, C. Hunter, 1991, Journal of molecular biology.

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

Gail J. Bartlett, J. Thornton, N. Borkakoti, 2003, Journal of molecular biology.

The CATH protein family database: A resource for structural and functional annotation of genomes

Frances M. G. Pearl, Daniel W. A. Buchan, David A. Lee, 2002, Proteomics.

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

Irene Papatheodorou, Janet M Thornton, Linda Partridge, 2011, Molecular systems biology.

Metal ions in biological catalysis: from enzyme databases to general principles

Janet M. Thornton, Gemma L. Holliday, Ivano Bertini, 2008, JBIC Journal of Biological Inorganic Chemistry.

Location of ‘continuous’ antigenic determinants in the protruding regions of proteins.

W R Taylor, D J Barlow, J M Thornton, 1986, The EMBO journal.

Shape variation in protein binding pockets and their ligands.

J. Thornton, R. Laskowski, A. Kahraman, 2007, Journal of molecular biology.

Transposable Element Landscape in Drosophila Populations Selected for Longevity

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2019, bioRxiv.

Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.

Janet M Thornton, Linda Partridge, J. Thornton, 2004, Protein engineering, design & selection : PEDS.

Correcting for sequence biases in present/absent calls

J. Thornton, L. Partridge, E. Schuster, 2007, Genome Biology.

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

Janet M Thornton, Linda Partridge, Eric Blanc, 2006, Genome Biology.

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

Frances M. G. Pearl, Daniel W. A. Buchan, David A. Lee, 2002, Genome research.

Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)

C. Orengo, J. Thornton, J. A. Ranea, 2006, Journal of Molecular Evolution.

Contemporary approaches to protein structure classification

David C. Jones, C. Orengo, D. T. Jones, 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

Protein folds and functions.

C. Orengo, S. Jones, J. Thornton, 1998, Structure.

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

Handan Melike Dönertaş, J. Thornton, M. Somel, 2020, Scientific Reports.

Meta-Analysis of the Gene Expression Profiles of Aging Brain Reveals Consistent Increase in Heterogeneity

Handan Melike Dönertaş, J. Thornton, M. Somel, 2019, bioRxiv.

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

Handan Melike Dönertaş, J. Thornton, M. Somel, 2019 .

The (non)malignancy of cancerous amino acidic substitutions

Martin S. Taylor, J. Thornton, David Talavera, 2010, Proteins.

Protein families and their evolution-a structural perspective.

C. Orengo, J. Thornton, 2005, Annual review of biochemistry.

Elucidating Human Phosphatase-Substrate Networks

J. Thornton, M. Wilmanns, M. Köhn, 2013, Science Signaling.

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

Angelo D. Favia, J. Thornton, F. Glaser, 2008, Journal of molecular biology.

Characterising Complex Enzyme Reaction Data

Handan Melike Dönertaş, J. Thornton, S. A. Rahman, 2015, bioRxiv.

Atlas of protein side-chain interactions

J. Thornton, Juswinder Singh, 1992 .

Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.

B. L. Sibanda, T. Blundell, J. Thornton, 1989, Journal of molecular biology.

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

C. Orengo, J. Thornton, E. Hutchinson, 1999, Journal of molecular biology.

Beta-hairpin families in globular proteins.

B. L. Sibanda, J. Thornton, 1985, Nature.

Helix geometry in proteins.

J. Thornton, D. Barlow, 1988, Journal of molecular biology.

Analysis and prediction of the different types of β-turn in proteins

J. Thornton, C. Wilmot, 1988 .

Analysis, design and modification of loop regions in proteins

B. L. Sibanda, J. Thornton, D. Barlow, 1988, BioEssays : news and reviews in molecular, cellular and developmental biology.

[5] Conformation of β hairpins in protein structures: Classification and diversity in homologous structures

B. L. Sibanda, J. Thornton, 1991 .

Accommodating sequence changes in beta-hairpins in proteins.

B. L. Sibanda, J. Thornton, 1993, Journal of molecular biology.

β-Hairpin families in globular proteins

B. L. Sibanda, J. Thornton, 1985, Nature.

A mutation data matrix for transmembrane proteins

David C. Jones, D. T. Jones, J. Thornton, 1994, FEBS letters.

Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins

J. Thornton, T. Massingham, S. Bhattacharyya, 2005, Genome Biology.

Analysis and prediction of the different types of beta-turn in proteins.

J. Thornton, C. Wilmot, 1988, Journal of molecular biology.

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

J. Thornton, E. Hutchinson, 1994, Protein science : a publication of the Protein Society.

Disulphide bridges in globular proteins.

J. Thornton, 1981, Journal of molecular biology.

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

J. Thornton, N. Luscombe, R. Laskowski, 1997, Nucleic acids research.

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

J. Thornton, H. Ponstingl, I. Nobeli, 2003, Journal of molecular biology.

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.

R. A. George, J. Thornton, R. Spriggs, 2005, Journal of molecular biology.

Understanding nature's catalytic toolkit.

J. Thornton, Alex Gutteridge, 2005, Trends in biochemical sciences.

The chemistry of protein catalysis.

Gemma L. Holliday, John B. O. Mitchell, J. Thornton, 2007, Journal of molecular biology.

Missing in action: enzyme functional annotations in biological databases.

J. Thornton, J. Garavelli, R. Apweiler, 2009, Nature chemical biology.

Protein promiscuity and its implications for biotechnology

Angelo D. Favia, J. Thornton, I. Nobeli, 2009, Nature Biotechnology.

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

Gemma L. Holliday, John B. O. Mitchell, J. Thornton, 2009, Journal of molecular biology.

The structures and physicochemical properties of organic cofactors in biocatalysis.

Gemma L. Holliday, J. Thornton, J. D. Fischer, 2010, Journal of molecular biology.

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis

Gemma L. Holliday, John B. O. Mitchell, J. Thornton, 2011, The FEBS journal.

The evolution of enzyme function in the isomerases

J. Thornton, I. Sillitoe, Nicholas Furnham, 2014, Current opinion in structural biology.

Exploring the Biological and Chemical Complexity of the Ligases

Gemma L. Holliday, J. Thornton, Nicholas Furnham, 2014, Journal of molecular biology.

EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions

Gemma L. Holliday, J. Thornton, Nicholas Furnham, 2014, Nature Methods.

Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?

J. Thornton, I. McDonald, S. Price, 1994, Journal of molecular biology.

Conformational diversity of ligands bound to proteins.

J. Thornton, G. Stockwell, Gareth Stockwell, 2006, Journal of molecular biology.

Evolution of protein function, from a structural perspective.

C. Orengo, J. Thornton, A. Todd, 1999, Current opinion in chemical biology.

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

J. Thornton, J. B. Mitchell, S. Moodie, 1996, Journal of molecular biology.

Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing

Irene Papatheodorou, Janet M. Thornton, Linda Partridge, 2012, PloS one.

Understanding enzyme function evolution from a computational perspective.

Jonathan D Tyzack, Janet M Thornton, Ian Sillitoe, 2017, Current opinion in structural biology.

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

Janet M. Thornton, Nicholas Furnham, Roman A. Laskowski, 2016, Journal of molecular biology.

The history of the CATH structural classification of protein domains

Ian Sillitoe, Christine Orengo, Janet Thornton, 2015, Biochimie.

The Classification and Evolution of Enzyme Function.

Janet M Thornton, Nicholas Furnham, Syed Asad Rahman, 2015, Biophysical journal.

Topology-based protein structure comparison using a pattern discovery technique

David Gilbert, Janet M. Thornton, David R. Westhead, 2000 .

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

D S Moss, J M Thornton, R A Laskowski, 1993, Journal of molecular biology.

The complement of enzymatic sets in different species.

Janet M Thornton, Shiri Freilich, Bissan Al-Lazikani, 2005, Journal of molecular biology.

Current challenges in genome annotation through structural biology and bioinformatics.

Janet M Thornton, Nicholas Furnham, J. Thornton, 2012, Current opinion in structural biology.

A bioinformatician's view of the metabolome.

Janet M Thornton, Irene Nobeli, J. Thornton, 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential

Janet M. Thornton, John B. O. Mitchell, Roman A. Laskowski, 1999 .

The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

Ian Sillitoe, Tony E. Lewis, Mark Dibley, 2009, Structure.

Characterising Complex Enzyme Reaction Data

Handan Melike Dönertaş, J. Thornton, S. A. Rahman, 2015, bioRxiv.

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

J. Thornton, S. Rees, R. Osborn, 1998, Biochemistry.

Distributions of water around amino acid residues in proteins.

J M Thornton, J. Thornton, N. Thanki, 1988, Journal of molecular biology.

Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.

J M Thornton, C M Dobson, J. Thornton, 1996, Journal of molecular biology.

Toward predicting protein topology: An approach to identifying β hairpins

Janet M. Thornton, Xavier de la Cruz, Adrian Shepherd, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Toward the detection and validation of repeats in protein structure

William R Taylor, Janet M Thornton, J. Thornton, 2004, Proteins.

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

Janet M Thornton, Susan Jones, J. Thornton, 2004, Nucleic acids research.

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

Janet M. Thornton, Christine A. Orengo, Natalie L. Dawson, 2016, Journal of molecular biology.

Knowledge-based prediction of protein structures and the design of novel molecules

T. L. Blundell, B. L. Sibanda, J. M. Thornton, 1987, Nature.

Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.

M J Rooman, S J Wodak, J M Thornton, 1989, Protein engineering.

Ligand selectivity and competition between enzymes in silico

Janet M Thornton, Irene Nobeli, Antonio Macchiarulo, 2004, Nature Biotechnology.

Atomic environments of arginine side chains in proteins.

J. Thornton, J. Singh, C. L. Nandi, 1993, Protein engineering.

Comparison of functional annotation schemes for genomes

Janet M. Thornton, Stuart C. G. Rison, J. Thornton, 2000, Functional & Integrative Genomics.

J M Thornton, C A Orengo, M B Swindells, 1995, Protein science : a publication of the Protein Society.

Alpha plus beta folds revisited: some favoured motifs.

C. Orengo, J. Thornton, Janet M. Thornton, 1993, Structure.

The shape of things to come?

Janet M. Thornton, J. Thornton, 1988, Nature.

Comparison of conformational characteristics in structurally similar protein pairs

T. P. Flores, C. Orengo, J. Thornton, 1993, Protein science : a publication of the Protein Society.

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

Janet M Thornton, Roman A Laskowski, Caroline F Wright, 2017, Molecular genetics & genomic medicine.

A combination of a functional motif model and a structural motif model for a database validation

Janet M. Thornton, Marialuisa Pellegrini-Calace, J. Thornton, 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

On the conformation of proteins: an analysis of β-pleated sheets

Janet M. Thornton, Michael J. E. Sternberg, M. Sternberg, 1977 .

On the conformation of proteins: the handedness of the connection between parallel beta-strands.

M J Sternberg, J M Thornton, M. Sternberg, 1977, Journal of molecular biology.

Analysis and prediction of carbohydrate binding sites.

J M Thornton, C Taroni, S. Jones, 2000, Protein engineering.

Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage.

J M Thornton, J. Thornton, G. P. Smith, 1998, Journal of molecular biology.

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

J M Thornton, R J Beynon, J. Thornton, 1998, Protein engineering.

Prediction of the location and type of β‐turns in proteins using neural networks

D Gorse, J M Thornton, J. Thornton, 1999, Protein science : a publication of the Protein Society.

Structure prediction and modelling.

J M Thornton, M B Swindells, M. Swindells, 1991, Current opinion in biotechnology.

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins

Janet M Thornton, Angelo D. Favia, Angelo D Favia, 2010, Proteins.

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

Nozomi Nagano, J. Thornton, E. Hutchinson, 1999, Protein science : a publication of the Protein Society.

Wavelet transforms for the characterization and detection of repeating motifs.

Denise Gorse, Janet M Thornton, J. Thornton, 2002, Journal of molecular biology.

Molecular modelling and epitope prediction of gp29 from lymphatic filariae.

J. Thornton, M. Zvelebil, M. Selkirk, 1993, Molecular and biochemical parasitology.

Emerging concepts in pseudoenzyme classification, evolution, and signaling

António J. M. Ribeiro, C. Orengo, J. Thornton, 2019, Science Signaling.

Identifying pseudoenzymes using functional annotation: pitfalls of common practice

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2020 .

Sequence and structural differences between enzyme and nonenzyme homologs.

Janet M Thornton, Annabel E. Todd, Christine A Orengo, 2002, Structure.

Protein folds, functions and evolution.

Frances M. G. Pearl, Annabel E. Todd, C. Orengo, 1999, Journal of molecular biology.

Protein Structure Classification

C. Orengo, J. Thornton, F. Pearl, 2015 .

Understanding the molecular machinery of genetics through 3D structures

Janet M. Thornton, Roman A. Laskowski, J. Thornton, 2008, Nature Reviews Genetics.

Drug repurposing for aging research using model organisms

J. Thornton, L. Partridge, D. Marcus, 2016, bioRxiv.

Drug repurposing for ageing research using model organisms

J. Thornton, L. Partridge, D. Marcus, 2016, bioRxiv.

Abstracting knowledge from the Protein Data Bank.

J. Thornton, R. Laskowski, Nicholas Furnham, 2013, Biopolymers.

Using structural motifs to identify proteins with DNA binding function

Jonathan A. Barker, J. Thornton, Susan Jones, 2003 .

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

Janet M Thornton, Helen M Berman, Susan Jones, 2003, Nucleic acids research.

Integrating Structure, Bioinformatics, and Enzymology to Discover Function

J. Thornton, R. Laskowski, A. Edwards, 2003, Journal of Biological Chemistry.

Towards fully automated structure-based function prediction in structural genomics: a case study.

Janet M Thornton, Christine Orengo, Roman A Laskowski, 2007, Journal of molecular biology.

Structural bioinformatics: from protein structure to function

J. Thornton, R. Laskowski, A. Edwards, 2007 .

Modelling by homology

Janet M. Thornton, Mark B. Swindells, M. Swindells, 1991 .

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

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2020, Mechanisms of Ageing and Development.

Common genetic associations between age-related diseases

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2020, Nature Aging.

Identifying Potential Ageing-Modulating Drugs In Silico

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2019, Trends in Endocrinology & Metabolism.

Gene expression‐based drug repurposing to target aging

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2018, Aging cell.

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

J. Thornton, L. Partridge, R. Williams, 2018, bioRxiv.

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

J. Thornton, M. Ziehm, Janet M. Thornton, 2013, Aging cell.

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

J. Thornton, J. Watson, 2009 .

2 . 2 Identifying catalytic domains in the PDB

R. A. George, M. Swindells, J. Thornton, 2004 .

The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.

J. Thornton, Karolina Pavic, M. Köhn, 2011, Biochemistry.

Evidence for lifespan extension and delayed age–related biomarkers in insulin receptor substrate 1 null mice

Linda Partridge, Colin Selman, Steven J. Lingard, 2008, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

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

Alex Gutteridge, Janet Thornton, J. Thornton, 2004, FEBS letters.

On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets.

M J Sternberg, J M Thornton, M. Sternberg, 1977, Journal of molecular biology.

Pathway evolution, structurally speaking.

Janet M Thornton, J. Thornton, S. C. Rison, 2002, Current opinion in structural biology.

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity

J. Thornton, G. Calamita, R. Oliva, 2010, Proceedings of the National Academy of Sciences.

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

Neera Borkakoti, Janet M. Thornton, Gemma L. Holliday, 2019, The Journal of Biological Chemistry.

Retrograde signaling is regulated by the dynamic interaction between Rtg2p and Mks1p.

J. Thornton, R. A. Butow, Zhengchang Liu, 2003, Molecular cell.

BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data

Janet M. Thornton, Mark J. Forster, John B. O. Mitchell, 1999, J. Comput. Chem..

Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.

J. Thornton, M. Zvelebil, D. Isenberg, 1996, Molecular immunology.

Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis

J. Thornton, L. Partridge, D. Ivanov, 2016, Cell reports.

Lithium Promotes Longevi ty through GSK 3 / NRF 2-Dependent Hormesis Graphical

J. Thornton, L. Partridge, D. Ivanov, 2016 .

Structural and sequence patterns in the loops of beta alpha beta units.

J M Thornton, J. Thornton, M. S. Edwards, 1987, Protein engineering.

Structural survey

Janet M. Thornton, J. Thornton, 1987, Nature.

Protein promiscuity and its implications for

Angelo D. Favia, J. Thornton, 2009 .

Evolutionary conservation of regulated longevity assurance mechanisms

Janet M Thornton, Linda Partridge, Colin Selman, 2007, Genome Biology.

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

T. P. Neufeld, J. Thornton, L. Partridge, 2020, PLoS genetics.

Exploring the chemistry and evolution of the isomerases

J. Thornton, S. A. Rahman, Sergio Martínez Cuesta, 2016, Proceedings of the National Academy of Sciences.

Proteins: interaction at a distance

J. Thornton, R. Laskowski, 2015, IUCrJ.

Cognate ligand domain mapping for enzymes.

Janet M Thornton, Irene Nobeli, Matthew Bashton, 2006, Journal of molecular biology.

Domain–ligand mapping for enzymes

J. Thornton, M. Bashton, 2009, Journal of molecular recognition : JMR.

A template search reveals mechanistic similarities and differences in β‐ketoacyl synthases (KAS) and related enzymes

Janet M Thornton, J. Thornton, C. T. Porter, 2003, Proteins.

Inferring protein function from structure.

Janet M Thornton, Gail J. Bartlett, Gail J Bartlett, 2003, Methods of biochemical analysis.

Heme proteins—Diversity in structural characteristics, function, and folding

Janet M Thornton, Abdullah Kahraman, Lorna J. Smith, 2010, Proteins.

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.

Janet M Thornton, Ivano Bertini, Claudia Andreini, 2009, Journal of molecular biology.

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.

Janet M Thornton, Sandra Orchard, Edmund Maser, 2009, Chemico-biological interactions.

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

Gemma L. Holliday, J. Thornton, Nicholas Furnham, 2013 .

The geometry of interactions between catalytic residues and their substrates.

Janet M Thornton, Gemma L. Holliday, John B. O. Mitchell, 2007, Journal of molecular biology.

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO

Janet M Thornton, Jennifer M. A. Tullet, Ian A Hope, 2010, Molecular systems biology.

Genome and proteome annotation: organization, interpretation and integration

Janet M Thornton, Gabrielle A. Reeves, David Talavera, 2009, Journal of The Royal Society Interface.

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

Janet M Thornton, Linda Partridge, Matías Fuentealba, 2018, bioRxiv.

In conversation with Janet Thornton

J. Thornton, P. Dhillon, 2020, The FEBS journal.

Protein Data Resources

J. Thornton, J. Garavelli, Nicholas Furnham, 2013 .

Alternative Splicing in the ENCODE Protein complement

Gabrielle A. Reeves, G. A. Reeves, Peter F. Hallin, 2008 .

From Structure to Function

C. Orengo, J. Thornton, M. Tress, 2021, Models of the Mind.

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins

J. Thornton, T. Massingham, Leon Goldovsky, 2006, Genome Biology.

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

J. Thornton, R. Laskowski, H. Firth, 2016, Human molecular genetics.

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.

N. P. Brown, C. Sander, J. Thornton, 1996, Trends in biochemical sciences.

Metabolic innovations towards the human lineage

J. Thornton, C. Ouzounis, Leon Goldovsky, 2008, BMC Evolutionary Biology.

Adenosine Triphosphate (ATP) Is a Candidate Signaling Molecule in the Mitochondria-to-Nucleus Retrograde Response Pathway

J. Thornton, Zhengchang Liu, F. Zhang, 2013, Genes.

RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast prion [URE3].

J. Thornton, R. A. Butow, Zhengchang Liu, 2002, Molecular biology of the cell.

Revised 11 / 27 / 01 RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS 1 and is linked to the formation of the yeast prion [ URE 3 ]

J. Thornton, R. A. Butow, Zhengchang Liu, 2002 .

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

J. Thornton, F. Raymond, M. A. Hasenahuer, 2019, bioRxiv.

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

J. Thornton, M. Pellegrini-Calace, 2005, Nucleic acids research.

The implications of alternative splicing in the ENCODE protein complement

Hagen Blankenburg, Fidel Ramírez, Thomas Lengauer, 2007, Proceedings of the National Academy of Sciences.

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

J. Thornton, A. Rosato, Nicholas Furnham, 2018, Journal of inorganic biochemistry.

An analysis of the three-dimensional structure of chicken triose phosphate isomerase.

M. Sternberg, J. Thornton, D. Phillips, 1977, Biochemical Society transactions.

Structural Patterns in Globular Proteins

J. Thornton, E. Hutchinson, A. L. Morris, 1994 .

Recurring structural motifs in proteins with different functions

T. P. Flores, J. M. Thornton, C. Orengo, 1993, Current Biology.

The fine details of evolution.

M. Sternberg, J. Thornton, R. Laskowski, 2009, Biochemical Society transactions.

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

António J. M. Ribeiro, J. Thornton, W. Reik, 2017, Nucleic acids research.

Regulation of Lifespan, Metabolism, and Stress Responses by the Drosophila SH2B Protein, Lnk

Janet M. Thornton, Linda Partridge, Daniela Wieser, 2010, PLoS genetics.

Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins

C. Orengo, J. Thornton, R. Laskowski, 2022, bioRxiv.

Protein-protein recognition via side-chain interactions.

T. Blundell, J. Thornton, J. Singh, 1988, Biochemical Society transactions.

EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2022, bioRxiv.

Progress towards recognising protein folds from amino acid sequence

William R. Taylor, David T. Jones, C Orengo, 1993 .

Smith, G.P. et al. Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. J. Mol. Biol. 277, 317-332

J. Thornton, G. Smith, G. Winter, 1998 .

Activation of the SPS Amino Acid-Sensing Pathway in Saccharomyces cerevisiae Correlates with the Phosphorylation State of a Sensor Component, Ptr3

J. Thornton, R. A. Butow, Zhengchang Liu, 2007, Molecular and Cellular Biology.

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

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2021, The FEBS journal.

EuroQSAR 2002: Designing Drugs and Crop Protectants: processes, problems and solution

Janet M. Thornton, Irene Nobeli, J. Thornton, 2003 .

Srinivasan (1962–2021) in Bioinformatics and beyond

J. Thornton, C. Orengo, R. Sowdhamini, 2022, Bioinform..

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

Alfonso Valencia, Karel Berka, Jaroslav Koča, 2019, Nucleic Acids Res..

BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential

Janet M. Thornton, John B. O. Mitchell, Roman A. Laskowski, 1999, J. Comput. Chem..

PDBsum: a Web-based database of summaries and analyses of all PDB structures.

M. L. Jones, E G Hutchinson, J M Thornton, 1997, Trends in biochemical sciences.

Protein domain superfolds and superfamilies

Janet M. Thornton, Christine A. Orengo, David T. Jones, 1994 .

AlphaFold2 protein structure prediction: Implications for drug discovery.

J. Thornton, N. Borkakoti, 2023, Current opinion in structural biology.

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

Jonathan D. Tyzack, Douglas E. V. Pires, António J. M. Ribeiro, 2022, Nucleic Acids Res..

Binding pocket shape analysis for protein function prediction

J. Thornton, A. Kahraman, R. Morris, 2005 .

Shape-based classification of bound ligands

J. Thornton, T. Funkhouser, R. Laskowski, 2022 .

The rapid generation of mutation data matrices from protein sequences

William R. Taylor, Janet M. Thornton, David T. Jones, 1992, Comput. Appl. Biosci..

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family

Janet M. Thornton, Rafael Najmanovich, Richard J. Morris, 2007, Bioinform..

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

J. Thornton, L. Partridge, A. Hingorani, 2021, Scientific Reports.

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

J M Thornton, R A Laskowski, A C Wallace, 1995, Protein engineering.

A nuclear magnetic resonance investigation of the conformation of nicotinamide mononucleotide in aqueous solution.

J. Thornton, J. Feeney, N. Birdsall, 1975, Journal of the American Chemical Society.

VarSite: Disease variants and protein structure

Janet M Thornton, Ian Sillitoe, James D Stephenson, 2019, Protein science : a publication of the Protein Society.

PDBsum: Structural summaries of PDB entries

Radka Svobodová Vařeková, Janet M Thornton, Radka Svobodová Vareková, 2017, Protein science : a publication of the Protein Society.

Protein Function Prediction by Matching Volumetric Models of Active Sites

J. Thornton, T. Funkhouser, R. Laskowski, 2006 .

Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network

Janet M. Thornton, Jonathan J. Ward, J. Thornton, 2007, PLoS Comput. Biol..

Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magnetic-resonance probes.

J. Thornton, R. J. Williams, P. Tanswell, 1975, European journal of biochemistry.

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.

J M Thornton, P J Sadler, J. Thornton, 1996, European journal of biochemistry.

Conformational energy calculations for dinucleotide molecules: A study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+)

J. Thornton, P. Bayley, Peter M. Bayley, 1977, Biopolymers.

Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate

J. Thornton, P. Bayley, 1976, Biopolymers.

A NUCLEAR MAGNETIC RESONANCE INVESTIGATION OF THE CONFORMATION OF NICOTINAMIDE MONONUCLEOTIDE IN AQUEOUS SOLUTION

J. Thornton, J. Feeney, N. Birdsall, 1975 .

Conformational studies of lanthanide complexes with carboxylate ligands

J. Thornton, ROBERT J. P. Williams, B. Levine, 1974 .

Calcium binding by troponin-C. A proton magnetic resonance study.

J. Thornton, B. Levine, D. Coffman, 1977, Journal of molecular biology.

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

J M Thornton, J. Thornton, S. Hubbard, 1991, Journal of molecular biology.

SCOPEC: a database of protein catalytic domains

Janet M. Thornton, Richard A. George, Bissan Al-Lazikani, 2004, ISMB/ECCB.

Amino and carboxy-terminal regions in globular proteins.

J M Thornton, B. L. Sibanda, J. Thornton, 1983, Journal of molecular biology.

Recurrence of a binding motif?

David T. Jones, C. Orengo, M. Swindells, 1993, Nature.

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

Christoph Steinbeck, Janet M. Thornton, Gemma L. Holliday, 2016, Bioinform..

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]

J. Thornton, J. McElwee, D. Gems, 2006, Mechanisms of Ageing and Development.

Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans

David Gems, Janet Thornton, Eric Blanc, 2006, Mechanisms of Ageing and Development.

A topological model for hepatitis B surface antigen.

C R Howard, J M Thornton, J. Thornton, 1992, Intervirology.

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons

Janet M. Thornton, Rafael Najmanovich, Richard J. Morris, 2005, Bioinform..

Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania

Ian H. Gilbert, Janet M. Thornton, Roman A. Laskowski, 1998, J. Comput. Aided Mol. Des..

Functional conservation in genes and pathways linking ageing and immunity

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2021, Immunity & ageing : I & A.

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

Janet M. Thornton, Nick Goldman, Roman A. Laskowski, 2013, PLoS Comput. Biol..

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

J. Thornton, R. Laskowski, Alison M. Male, 2017, Human molecular genetics.

Comparison of the calcium- and magnesium-induced structural changes of troponin--C. A proton magnetic resonance study.

J. Thornton, D. Mercola, B. Levine, 1978, Biochimica et biophysica acta.

Proton magnetic resonance study of troponin‐C

J. Thornton, B. Levine, Barry A. Levine, 1976, FEBS letters.

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

J. Thornton, T. Pons, R. Laskowski, 2021, Scientific Reports.

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Frances M. G. Pearl, Andrew P. Harrison, David A. Lee, 2004, Nucleic Acids Res..

Validation of protein models derived from experiment.

J M Thornton, R A Laskowski, J. Thornton, 1998, Current opinion in structural biology.

A new approach to protein fold recognition

D. T. Jones, J. M. Thornton, David C. Jones, 1992, Nature.

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

Janet M. Thornton, Bekim Sadikovic, Sanaa Choufani, 2019, Genome Biology.

Factors limiting the performance of prediction‐based fold recognition methods

J. Thornton, Janet M. Thornton, Xavier De La Cruz, 2008, Protein science : a publication of the Protein Society.

Target Selection and Determination of Function in Structural Genomics

Christine Orengo, James Bray, Aled Edwards, 2003, IUBMB life.

Retrograde Response to Mitochondrial Dysfunction Is Separable from TOR1/2 Regulation of Retrograde Gene Expression*

Janet Thornton, J. Thornton, S. Giannattasio, 2005, Journal of Biological Chemistry.

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data

Stijn van Dongen, Anton J. Enright, Tom C. Freeman, 2007, PLoS Comput. Biol..

Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level

Nicholas M. Luscombe, Janet M. Thornton, Roman A. Laskowski, 2001, Nucleic Acids Res..

A structural biology community assessment of AlphaFold2 applications

Douglas E. V. Pires, Norman E. Davey, Carlos H. M. Rodrigues, 2021, bioRxiv.

Domain assignment for protein structures using a consensus approach: Characterization and analysis

J M Thornton, M B Swindells, S Jones, 1998, Protein science : a publication of the Protein Society.

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans

Irene Papatheodorou, Janet M. Thornton, Jennifer M. A. Tullet, 2014, Aging.

Conservation helps to identify biologically relevant crystal contacts.

J M Thornton, W S Valdar, J. Thornton, 2001, Journal of molecular biology.

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

W R Taylor, D T Jones, J M Thornton, 1994, Biochemistry.

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

Handan Melike Dönertaş, J. Thornton, M. Somel, 2020, Scientific Reports.

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

J. Thornton, V. Kedlian, Handan Melike Donertas, 2019, Aging.

Using the CATH domain database to assign structures and functions to the genome sequences.

J M Thornton, M B Swindells, A A Salamov, 2000, Biochemical Society transactions.

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

Mona Singh, Thomas A. Funkhouser, Janet M. Thornton, 2009, PLoS Comput. Biol..

TORC2 Signaling Is Antagonized by Protein Phosphatase 2A and the Far Complex in Saccharomyces cerevisiae

J. Thornton, Zhengchang Liu, Tammy Pracheil, 2012, Genetics.

TORC2 Signaling is Antagonized by Protein Phosphatase 2A and the Far Complex in S. cerevisiae

J. Thornton, Zhengchang Liu, Tammy Pracheil, 2012 .

Evolution of enzymes and pathways for the biosynthesis of cofactors.

Gemma L. Holliday, J. Thornton, F. Rébeillé, 2007, Natural product reports.

New tools and resources for analysing protein structures and their interactions.

N M Luscombe, J M Thornton, D R Westhead, 1998, Acta crystallographica. Section D, Biological crystallography.

Ribosomal Protein S6 Kinase 1 Signaling Regulates Mammalian Life Span

Janet M. Thornton, David Carling, Linda Partridge, 2009, Science.

Assigning genomic sequences to CATH

James E. Bray, Frances M. G. Pearl, Andrew P. Harrison, 2000, Nucleic Acids Res..

From Structure to Function

C. Orengo, J. Thornton, M. Tress, 2021, Models of the Mind.

Microeconomic Principles Explain an Optimal Genome Size in Bacteria

Janet M. Thornton, Christine A. Orengo, Juan Garcia Ranea, 2004, Spanish Bioinformatics Conference.

The CATH Database provides insights into protein structure/function relationships

James E. Bray, Frances M. G. Pearl, Annabel E. Todd, 1999, Nucleic Acids Res..

From Genome to Function

J M Thornton, J. Thornton, 2001, Science.

Peptide–protein interactions: an overview

J M Thornton, J. Thornton, M. Zvelebil, 1993, Quarterly Reviews of Biophysics.

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

Janet M. Thornton, Nicholas Furnham, Nidhi Tyagi, 2015, PLoS Comput. Biol..

Substrate recognition by proteinases.

J. Thornton, S. Hubbard, S. Campbell, 1992, Faraday discussions.

The European Bioinformatics Institute’s data resources

Catherine Brooksbank, Janet M. Thornton, Graham Cameron, 2009, Nucleic Acids Res..

Longevity GWAS Using the Drosophila Genetic Reference Panel

J. Thornton, L. Partridge, T. Mackay, 2015, The journals of gerontology. Series A, Biological sciences and medical sciences.

Prediction of progress at last

Janet M. Thornton, T. P. Flores, David T. Jones, 1991, Nature.

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

Chris Sander, Shoshana J. Wodak, Jean Richelle, 1998, Journal of molecular biology.

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Ian Sillitoe, Janet M. Thornton, 2014, Nucleic Acids Res..

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

Catherine Brooksbank, Janet M. Thornton, Graham Cameron, 2004, Nucleic Acids Res..

Recognition of super-secondary structure in proteins.

W R Taylor, J M Thornton, J. Thornton, 1984, Journal of molecular biology.

Minimum information about a bioactive entity (MIABE)

Peter Murray-Rust, John P. Overington, Henning Hermjakob, 2011, Nature Reviews Drug Discovery.

X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.

J M Thornton, R A Laskowski, J. Thornton, 1996, Journal of molecular biology.

Long loops in proteins.

J M Thornton, J. Thornton, K. Toda, 1995, Protein engineering.

Accommodating sequence changes in β-hairpins in proteins

B. L. Sibanda, J. Thornton, 1993 .

Lessons from analyzing protein structures

Janet M. Thornton, J. Thornton, 1992 .

Using mechanism similarity to understand enzyme evolution

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2022, Biophysical Reviews.

Interactive map projection algorithm for illustrating protein surfaces

J. Thornton, D. Barlow, 1986 .

Small-molecule metabolism: an enzyme mosaic.

J M Thornton, C Chothia, C. Chothia, 2001, Trends in biotechnology.

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2012, PLoS Comput. Biol..

PROCHECK: validation of protein‐structure coordinates

Janet M. Thornton, Roman A. Laskowski, Malcolm W. MacArthur, 2012 .

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids

Janet M. Thornton, Roman A. Laskowski, Victor V. Chistyakov, 2004, Nucleic Acids Res..

The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2008, Nucleic Acids Res..

PROCOGNATE: a cognate ligand domain mapping for enzymes

Janet M. Thornton, Irene Nobeli, Matthew Bashton, 2007, Nucleic Acids Res..

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

Roland L. Dunbrack, Thomas A. Hopf, Leandro G. Radusky, 2021, Nucleic Acids Res..

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

Janet M Thornton, J. Thornton, Gordon S Whamond, 2006, Journal of molecular biology.

MACiE: a database of enzyme reaction mechanisms

Peter Murray-Rust, Janet M. Thornton, Gemma L. Holliday, 2005, Bioinform..

ELIXIR: a distributed infrastructure for European biological data.

Janet M Thornton, Lindsey C Crosswell, L. C. Crosswell, 2012, Trends in biotechnology.

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

J. Thornton, L. Partridge, D. Ivanov, 2021, Proceedings of the National Academy of Sciences.

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

J M Thornton, R A Laskowski, D Milburn, 1998, Protein engineering.

On the molecular discrimination between adenine and guanine by proteins.

J M Thornton, R A Laskowski, I Nobeli, 2001, Nucleic acids research.

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

Janet M. Thornton, Rafael Najmanovich, Natalja Kurbatova, 2008, ECCB.

Methods to characterize the structure of enzyme binding sites

Janet M. Thornton, Abdullah Kahraman, J. Thornton, 2008 .

Protein Engineering '87—conference report

Janet M. Thornton, Michael J. Gait, Ronald Wetzel, 1987 .

Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy

Janet M. Thornton, Roman A. Laskowski, Malcolm W. MacArthur, 1994 .

Insights into protein evolution and function from the CATH structural database

James E. Bray, Frances M. G. Pearl, David A. Lee, 2001 .

Software Tools for Protein Structure Analysis and Fold Classification

Janet M. Thornton, Christine A. Orengo, Roman A. Laskowski, 1999 .

Faculty Opinions recommendation of A simple physical model for the prediction and design of protein-DNA interactions.

Janet M. Thornton, J. Thornton, 2004 .

The future of bioinformatics

Janet M. Thornton, J. Thornton, 1998 .

Faculty Opinions recommendation of A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology.

Janet M. Thornton, J. Thornton, 2004 .

Faculty Opinions recommendation of Sputnik: a database platform for comparative plant genomics.

Janet M. Thornton, J. Thornton, 2003 .

PDBsum additions

Karel Berka, Janet M. Thornton, Roman A. Laskowski, 2013, Nucleic Acids Res..

Small Molecule Subgraph Detector (SMSD) toolkit

Rainer Schrader, Janet M. Thornton, Gemma L. Holliday, 2009, J. Cheminformatics.

Analysis and modelling of antibodies.

Janet M. Thornton, Acr Martin, Rm MacCallum, 1995 .

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

J. Thornton, Ioannis G. Riziotis, 2022, Protein science : a publication of the Protein Society.

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

Janet M. Thornton, Gemma L. Holliday, Gabriele Cavallaro, 2009, Bioinform..

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

Peter Murray-Rust, Janet M. Thornton, Gemma L. Holliday, 2006, Nucleic Acids Res..

Faculty Opinions recommendation of Apollo: a sequence annotation editor.

Janet M. Thornton, J. Thornton, 2003 .

Structure‐Based Prediction of Enzymes and Their Active Sites

Janet M. Thornton, James Torrance, James W. Torrance, 2008 .

Protein-DNA Interactions

Helen M. Berman, Janet M. Thornton, Susan Jones, 1999 .

Faculty Opinions recommendation of Building an automated classification of DNA-binding protein domains.

Janet M. Thornton, J. Thornton, 2002 .

Coordination of structural bioinformatics activities across Europe

Sameer Velankar, Shoshana J. Wodak, Janet M. Thornton, 2018, Acta Crystallographica Section A: Foundations and Advances.

The Impact of Structural Proteomics on Macromolecular Structure Databases

Janet M. Thornton, James D. Watson, J. Thornton, 2008 .

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

Frances M. G. Pearl, Ian Sillitoe, Janet M. Thornton, 2006, Nucleic Acids Res..

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

Janet M. Thornton, James D. Watson, Roman A. Laskowski, 2005, Nucleic Acids Res..

Bridging cheminformatics and bioinformatics by using protein structures.

Janet M. Thornton, Awe Chan, Roman A. Laskowski, 2001 .

Faculty Opinions recommendation of Computational comparison of two mouse draft genomes and the human golden path.

Janet M. Thornton, J. Thornton, 2003 .

A public regulator of longevity acts via lineage-specific effectors.

Janet M. Thornton, Dominic J. Withers, Eric Blanc, 2006 .

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

Irene Papatheodorou, Janet M. Thornton, Rudolfs Petrovs, 2014, Bioinform..

[Invited Lecture] Protein Folds and Functions

Janet M. Thornton, Christine A. Orengo, Roman A. Laskowski, 1998, German Conference on Bioinformatics.

SurvCurv database and online survival analysis platform update

Janet M. Thornton, Linda Partridge, Matthias Ziehm, 2015, Bioinform..

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

J. Thornton, L. Partridge, D. Ivanov, 2017, PLoS genetics.

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

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

Recognizing the fold of a protein structure

Frances M. G. Pearl, Andrew P. Harrison, Ian Sillitoe, 2003, Bioinform..

Motif-based searching in TOPS protein topology databases

David R. Gilbert, Janet M. Thornton, David R. Westhead, 1999, Bioinform..

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

J M Thornton, D R Westhead, D C Hatton, 1998, Trends in biochemical sciences.

An algorithm for automatically generating protein topology cartoons.

T. P. Flores, J M Thornton, T P Flores, 1994, Protein engineering.

Structures in the AKH Family of Neuropeptides

J. Thornton, C. Wilmot, A. Drake, 1990 .

THE RAMACHANDRAN PLOT AND PROTEIN STRUCTURE VALIDATION

J. Thornton, R. Laskowski, Nicholas Furnham, 2013 .

PDBsum extras: SARS‐CoV‐2 and AlphaFold models

J. Thornton, R. Laskowski, 2021, Protein science : a publication of the Protein Society.

ELIXIR - A European Infrastructure for Biological Information: Challenges and Progress

Janet M. Thornton, J. Thornton, 2009, GI Jahrestagung.

SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis

J. Thornton, P. Moreno, I. Papatheodorou, 2023, NAR genomics and bioinformatics.

An examination of the conservation of surface patch polarity for proteins

Janet M. Thornton, Hugh P. Shanahan, J. Thornton, 2004, Bioinform..

Faculty Opinions recommendation of Enzyme family classification by support vector machines.

Janet M. Thornton, J. Thornton, 2004 .

Protein folds and their recognition from sequence

Janet M. Thornton, Christine A. Orengo, David T. Jones, 1996 .

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

Jennifer M. A. Tullet, J. Thornton, Alexandre Benedetto, 2014, PLoS genetics.

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

Janet M. Thornton, Susan Jones, J. Thornton, 2003, Comparative and Functional Genomics.

PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure

Janet M. Thornton, Marialuisa Pellegrini-Calace, Tim Maiwald, 2009, PLoS Comput. Biol..

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

Janet M. Thornton, Romina Oliva, Marialuisa Pellegrini-Calace, 2009, Bioinform..

Classifying a Protein Fold in the CATH Hierarchic Database

Janet M. Thornton, Christine A. Orengo, Acr Martin, 1998 .

The European Bioinformatics Institute: Leading the bioinformatics revolution

Janet M. Thornton, Graham Cameron, Cath Brooksbank, 2004 .

Faculty Opinions recommendation of A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.

Janet M. Thornton, J. Thornton, 2003 .

Case Studies: Function Predictions of Structural Genomics Results

Janet M. Thornton, James D. Watson, J. Thornton, 2009 .

Protein function prediction using local 3D templates.

Janet M Thornton, Roman A Laskowski, James D Watson, 2005, Journal of molecular biology.

A rapid algorithm for generating minimal pathway distances

Lazaros G. Papageorgiou, Janet M. Thornton, Idl Bogle, 2001, Intelligent Systems in Molecular Biology.

Faculty Opinions recommendation of Calmodulin target database.

Janet M. Thornton, J. Thornton, 2003 .

Integrating biological data through the genome.

Janet M Thornton, G. A. Reeves, J. Thornton, 2006, Human molecular genetics.

Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity

J. Thornton, L. Partridge, D. Ivanov, 2017, Cell reports.

Living longer by dieting: analysis of transcriptional response after caloric restriction

Janet M. Thornton, Linda Partridge, Dominic J. Withers, 2005, BMC Bioinformatics.

Classifying a protein in the CATH database of domain structures.

D T Jones, J M Thornton, C A Orengo, 1998, Acta crystallographica. Section D, Biological crystallography.

Derivation of 3D coordinate templates for searching structural databases: Application to ser‐His‐Asp catalytic triads in the serine proteinases and lipases

J M Thornton, R A Laskowski, A C Wallace, 1996, Protein science : a publication of the Protein Society.

A novel degron-mediated degradation of the RTG pathway regulator, Mks1p, by SCFGrr1.

J. Thornton, R. A. Butow, Zhengchang Liu, 2005, Molecular biology of the cell.

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2010, Nucleic Acids Res..

1H NMR structure of an antifungal γ‐thionin protein SIα1: Similarity to scorpion toxins

J M Thornton, C Bloch, S U Patel, 1998, Proteins.

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis

Janet M. Thornton, Jonathan A. Barker, J. Thornton, 2003, Bioinform..

An ellipsoidal approximation of protein shape

William R. Taylor, J M Thornton, J. Thornton, 1983 .

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

J. Thornton, R. Laskowski, Pilar Cossio, 2021, Frontiers in Molecular Biosciences.

From protein structure to biochemical function?

Janet M. Thornton, James D. Watson, Roman A. Laskowski, 2004, Journal of Structural and Functional Genomics.

The CATH database: an extended protein family resource for structural and functional genomics

James E. Bray, Frances M. G. Pearl, Nigel J. Martin, 2003, Nucleic Acids Res..

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

J M Thornton, R A Laskowski, J. Thornton, 1997, Proteins.

Shared structural motif in proteins

David T. Jones, C. Orengo, M. Swindells, 1993, Nature.

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

António J. M. Ribeiro, J. Thornton, N. Borkakoti, 2021, bioRxiv.

Introduction. Bioinformatics: from molecules to systems

Janet M Thornton, Michael J E Sternberg, David T. Jones, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Activating transcription factor 4-dependent lactate dehydrogenase activation as a protective response to amyloid beta toxicity

J. Thornton, L. Partridge, D. Fabian, 2021, Brain communications.

Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.

Steven J. Lingard, J. Thornton, L. Partridge, 2006, Physiological genomics.

Secondary and Supersecondary Motifs in Protein Structures

Janet M. Thornton, B. L. Sibanda, Bancinyane L. Sibanda, 1992 .

Modelling antibody combining sites: a review.

J M Thornton, J. Thornton, 2007, Ciba Foundation symposium.

Tackling a loopy problem

J. Thornton, 1990, Nature.

Three-dimensional structural aspects of the design of new protein molecules

Michael J. E. Sternberg, B. L. Sibanda, Thomas Leon Blundell, 1986, Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences.

Prediction of super-secondary structure in proteins

J. M. Thornton, J. Thornton, W. Taylor, 1983, Nature.

On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets.

M J Sternberg, J M Thornton, M. Sternberg, 1977, Journal of molecular biology.

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

J M Thornton, David C. Jones, J. Thornton, 1995, Proteins.

Structural and sequence patterns in the loops of βαβ units

Janet M. Thornton, Michael J. E. Sternberg, M. Sternberg, 1987 .

The European Bioinformatics Institute’s data resources 2014

Rolf Apweiler, Catherine Brooksbank, Janet M. Thornton, 2013, Nucleic Acids Res..

Analysis and prediction of membrane protein structure

J. Thornton, L. Partridge, T. Eyre, 2004 .

The influence of tertiary structure on secondary structure prediction

J. Thornton, W. Taylor, R. Garratt, 1985 .

Protein structures and complexes: what they reveal about the interactions that stabilize them

John B. O. Mitchell, David T. Jones, J. Thornton, 1993, Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences.

Prediction of protein structure from amino acid sequence

Janet M. Thornton, Michael J. E. Sternberg, M. Sternberg, 1978, Nature.

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

Janet M. Thornton, Nicholas Furnham, Gemma L. Holliday, 2017, Nucleic Acids Res..

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

Janet M Thornton, James W Torrance, James W. Torrance, 2008, Proteins.

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

J M Thornton, C A Orengo, A D Michie, 1996, Journal of molecular biology.

Towards an understanding of the arginine-aspartate interaction.

J M Thornton, J. Thornton, Juswinder Singh, 1992, Journal of molecular biology.

The Greek key motif: extraction, classification and analysis.

E G Hutchinson, J M Thornton, J. Thornton, 1993, Protein engineering.

HERA—A program to draw schematic diagrams of protein secondary structures

E G Hutchinson, J M Thornton, J. Thornton, 1990, Proteins.

Chapter 4 – Molecular Sociology

J. Thornton, I. Nooren, 2003 .

An automated protocol for modelling peptide substrates to proteases

Janet M. Thornton, Rodrigo Ochoa, Pilar Cossio, 2020, BMC Bioinformatics.

Exploring Chemical Biosynthetic Design Space with Transform-MinER.

Neera Borkakoti, Janet M Thornton, Jonathan D. Tyzack, 2019, ACS synthetic biology.

Protein structure prediction.

J M Thornton, D R Westhead, J. Thornton, 1998, Current opinion in biotechnology.

Sequences and topology

M. Gerstein, J. Thornton, 1991, Current Opinion in Structural Biology.

Large-scale Annotation of Biochemically Relevant Pockets and Tunnels in Cognate Enzyme-Ligand Complexes

J. Thornton, J. Damborský, O. Vávra, 2023, bioRxiv.

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

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2018, Nucleic Acids Res..

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

Neera Borkakoti, Janet M. Thornton, Jonathan D. Tyzack, 2018, Structure.

The CoFactor database: organic cofactors in enzyme catalysis

Janet M. Thornton, Gemma L. Holliday, Julia D. Fischer, 2010, Bioinform..

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

Janet M. Thornton, Nicholas Furnham, Julius O. B. Jacobsen, 2013, Nucleic Acids Res..

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

J. Thornton, V. Kedlian, Handan Melike Donertas, 2019, bioRxiv.

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

J. Thornton, L. Partridge, Julie Williams, 2020, PloS one.

Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

Janet M. Thornton, Abdellah Allali-Hassani, Alexander N. Plotnikov, 2007, PLoS Biology.

Modelling the interactions of protein side-chains

John B. O. Mitchell, J. Thornton, S. Price, 1995 .

Structures of N‐termini of helices in proteins

J. Thornton, A. Doig, B. Stapley, 1997, Protein science : a publication of the Protein Society.

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

J. Thornton, N. Thanki, J. Goodfellow, 1991, Journal of molecular biology.

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

Janet M Thornton, Rafael J Najmanovich, James W Torrance, 2005, BioTechniques.

A comparison of three theoretical approaches to the study of side-chain interactions in proteins

John B. O. Mitchell, J. Thornton, Juswinder Singh, 1993 .

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

W R Taylor, J M Thornton, J. Thornton, 1991, FEBS Letters.

Macromolecular structure information and databases

Christopher J. Rawlings, Shoshana J. Wodak, Jean Richelle, 1996 .

Rebuilding flavodoxin from Cα coordinates: A test study

Janet M. Thornton, J. Thornton, L. Reid, 1989 .

SPINE bioinformatics and data‐management aspects of high‐throughput structural biology

A. Rachedi, R. J. Morris, C. Cambillau, 2006, Acta crystallographica. Section D, Biological crystallography.

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

Janet M. Thornton, Carles Ferrer-Costa, Hugh P. Shanahan, 2005, Bioinform..

Gene3D: structural assignments for the biologist and bioinformaticist alike

James E. Bray, Frances M. G. Pearl, Daniel W. A. Buchan, 2003, Nucleic Acids Res..

Hydration of Amino Acids in Protein Crystals

J. Thornton, N. Thanki, J. Goodfellow, 1993 .

Iditis: protein structure database.

J Thornton, S Gardner, J. Thornton, 1998, Acta crystallographica. Section D, Biological crystallography.

Preliminary Analysis of Water Molecule Distributions in Proteins

J. Thornton, N. Thanki, J. Goodfellow, 1989 .

1,000 structures and more from the MCSG

Janet M Thornton, David A. Lee, Roman A Laskowski, 2011, BMC Structural Biology.

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

Janet M Thornton, James D Stephenson, Roman A Laskowski, 2019, Bioinform..

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

J M Thornton, J. Thornton, N. Thanki, 1990, Protein engineering.

Gene expression‐based drug repurposing to target aging

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2018, Aging cell.

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

Janet M Thornton, Evangelos Simeonidis, Lazaros G Papageorgiou, 2003, Metabolic engineering.

Gene Expression-Based Drug Repurposing to Target Ageing

Handan Melike Dönertaş, J. Thornton, L. Partridge, 2018, bioRxiv.

The new science of ageing

Linda Partridge, Janet Thornton, J. Thornton, 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate.

J M Thornton, J. Thornton, P. Bayley, 1975, The Biochemical journal.

Morphological aspects of oligorneric protein structures

J. Thornton, D. Gorse, H. Ponstingl, 2005 .

Identifying pseudoenzymes using functional annotation: pitfalls of common practice

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2019, The FEBS journal.

Modelling protein unfolding: hen egg-white lysozyme.

J M Thornton, J. Thornton, J. Goodfellow, 1997, Protein engineering.

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

David A. Lee, Ian Sillitoe, Janet M. Thornton, 2012, Nucleic Acids Res..

Software engineering challenges in bioinformatics

Janet M. Thornton, Jonathan A. Barker, J. Thornton, 2004, Proceedings. 26th International Conference on Software Engineering.

Protein Evolution: Sequences, Structures and Systems

J. Thornton, R. Laskowski, 2009 .

Sequences and topology.

Mark Gerstein, Janet M. Thornton, M. Gerstein, 2001, Current opinion in structural biology.

BLEEP—potential of mean force describing protein–ligand interactions: II. Calculation of binding energies and comparison with experimental data

Janet M. Thornton, Mark J. Forster, John B. O. Mitchell, 1999 .

A rapid classification protocol for the CATH Domain Database to support structural genomics

James E. Bray, Frances M. G. Pearl, Nigel J. Martin, 2001, Nucleic Acids Res..

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

Denise Gorse, Janet M Thornton, Adrian J Shepherd, 2002, Proteins.

An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase.

M. Sternberg, J. Thornton, D. Phillips, 1978, Journal of molecular biology.

Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic.

J. Thornton, J. Uppenbrink, J. H. Viles, 2009, International journal of peptide and protein research.

Protein folds: towards understanding folding from inspection of native structures.

D. T. Jones, M. Swindells, J. Thornton, 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

Design, synthesis and structure of a zinc finger with an artificial beta-turn.

J. Thornton, J. Uppenbrink, J. H. Viles, 1998, Journal of molecular biology.

Molecular basis for DPY-30 association to COMPASS-like and NURF complexes.

J. Thornton, A. Shilatifard, M. Brand, 2014, Structure.

PROTEIN NUCLEIC ACID INTERACTIONS GRANT # DE-FG02-96ER62166 FINAL REPORT

J. Thornton, H. Berman, 2005 .

The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

António J. M. Ribeiro, J. Thornton, N. Borkakoti, 2023, bioRxiv.

Electrostatic interactions in proteins

J. Thornton, 1982, Nature.

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

J M Thornton, B. L. Sibanda, J. Thornton, 1991, Methods in enzymology.

Protein Quaternary Structure: Subunit–Subunit Interactions

J. Thornton, Susan Jones, 2001 .

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Tony E. Lewis, Alison L. Cuff, 2014, Nucleic Acids Research.

The EBI enzyme portal

Christoph Steinbeck, Maria Jesus Martin, Claire O'Donovan, 2012, Nucleic Acids Res..

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster † †Electronic supplementary information (ESI) available. See DOI: 10.1039/c3mb25485b Click here for additional data file.

Irene Papatheodorou, Janet M. Thornton, Matthias Ziehm, 2013, Molecular bioSystems.

Structural genomics takes off.

J Thornton, J. Thornton, J. Thornton, 2001, Trends in biochemical sciences.

Protein fold recognition by sequence threading: tools and assessment techniques

D T Jones, J M Thornton, R T Miller, 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Variability, Modelling and Prediction of β-Hairpins with Reference to the Immunoglobulin Fold

B. L. Sibanda, J. Thornton, W. Taylor, 1985 .

The Protein Feature Ontology: a tool for the unification of protein feature annotations

Andreas Prlic, Karen Eilbeck, Claire O'Donovan, 2008, Bioinform..

Genome-wide responses to mitochondrial dysfunction.

Varshal K. Davé, H R Garner, J. Thornton, 2001, Molecular biology of the cell.

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

J M Thornton, F Eisenmenger, J. Thornton, 1994, Protein science : a publication of the Protein Society.

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

J M Thornton, J Saldanha, J. Thornton, 1991, Protein engineering.

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

J. Thornton, S. Moodie, 1993, Nucleic acids research.

Depicting topology and handedness in jellyroll structures

J. Thornton, E. Hutchinson, D. Woolfson, 1992, FEBS letters.

Current challenges in genome annotation through structural biology and bioinformatics.

J. Thornton, Nicholas Furnham, T. A. D. de Beer, 2012, Current opinion in structural biology.

Heme proteins—Diversity in structural characteristics, function, and folding

Lorna J. Smith, J. Thornton, A. Kahraman, 2010, Proteins.

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Tony E. Lewis, Jonathan G. Lees, 2014, Nucleic Acids Res..

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

J. Thornton, L. Partridge, I. Papatheodorou, 2011, Molecular systems biology.

The Classification and Evolution of Enzyme Function.

J. Thornton, Nicholas Furnham, S. A. Rahman, 2015, Biophysical journal.

Conformational changes observed in enzyme crystal structures upon substrate binding.

J. Thornton, Alex Gutteridge, 2005, Journal of molecular biology.

On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit.

M J Sternberg, J M Thornton, M. Sternberg, 1976, Journal of molecular biology.

Amino/aromatic interactions

John B. O. Mitchell, J. Thornton, Juswinder Singh, 1993, Nature.

Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere

Richard N. Armstrong, Patricia C. Babbitt, Eyal Akiva, 2014, PLoS biology.

Topological and stereochemical restrictions in β-sandwich protein structures

Janet M. Thornton, Derek N. Woolfson, J. Thornton, 1993 .

The distribution of charged groups in proteins

D J Barlow, J M Thornton, J. Thornton, 1986, Biopolymers.

DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.

Annabel E. Todd, J M Thornton, C A Orengo, 1999, Protein engineering.

Conformational Energy Calculations for Dinucleotide Molecules A STUDY OF THE COMPONENT MONONUCLEOTIDES ADENOSINE 5'-MONOPHOSPHATE. NICOTINAMIDE MONONUCLEOTIDE AND ADENOSINE 3'-MONOPHOSPHATE

J. Thornton, P. Bayley, 2005 .

Rebuilding flavodoxin from C alpha coordinates: a test study.

J M Thornton, J. Thornton, L. Reid, 1989, Proteins.

The history of the CATH structural classification of protein domains

C. Orengo, J. Thornton, I. Sillitoe, 2015, Biochimie.

Conformation of terminal regions in proteins

Janet M. Thornton, J. Thornton, Bancinyane L. Chakauya, 1982, Nature.

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2011, Nucleic Acids Res..

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

Jonathan D Tyzack, Janet M Thornton, Ian Sillitoe, 2018, Methods in molecular biology.

Faculty Opinions recommendation of Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.

J. Thornton, 2003 .

Modelling protein unfolding: A solvent insertion protocol

J. Thornton, Mark A. Williams, J. Goodfellow, 1996 .