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Kahraman, A. and Morris, R.J. and Laskowski, R.A. and Favia, A.D. and Thornton, Janet M. (2010) On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins 78 (5), pp. 1120-1136. ISSN 1097-0134.

Bashton, M. and Thornton, Janet M. (2010) Domain ligand mapping for enzymes. Journal of Molecular Recognition 23 (2), pp. 194-208. ISSN 1099-1352.

Oliva, R. and Calamita, G. and Thornton, Janet M. and Pellegrini-Calace, M. (2010) Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity. Proceedings of the National Academy of Sciences of the United States of America 107 (9), pp. 4135-4140. ISSN 0027-8424.

Slack, C. and Werz, C. and Wieser, D. and Alic, N. and Foley, A. and Stocker, H. and Withers, D.J. and Thornton, Janet M. and Hafen, E. and Partridge, L. (2010) Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk. PLoS Genetics 6 (3), n/a-n/a. ISSN 1553-7404.

Talavera, D. and Taylor, M.S. and Thornton, Janet M. (2010) The (non)malignancy of cancerous amino acidic substitutions. Proteins 78 (3), pp. 518-529. ISSN 1097-0134.

Brooksbank, C. and Cameron, G. and Thornton, Janet M. (2010) The European Bioinformatics Institute's data resources. Nucleic Acids Research 38 (1(S)), D17-D25. ISSN 0305-1048.

Oliva, R. and Thornton, Janet M. and Pellegrini-Calace, M. (2009) PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins. Bioinformatics 25 (23), pp. 3183-3184. ISSN 1367-4811.

Capra, J.A. and Laskowski, R.A. and Thornton, Janet M. and Singh, M. and Funkhouser, T.A. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Computational Biology 5 (12), ISSN 1553-7358.

Macchiarulo, A. and Thornton, Janet M. and Nobeli, Irene (2009) Mapping human metabolic pathways in the small molecule chemical space. Journal of Chemical Information and Modelling 49 (10), pp. 2272-2289. ISSN 1549-9596.

Selman, C. and Tullet, J.M.A. and Wieser, D. and Irvine, E. and Lingard, S.J. and Choudhury, A.I. and Claret, M. and Al-Qassab, H. and Carmignac, D. and Ramadani, F. and Woods, A. and Robinson, I.C.A. and Schuster, E. and Batterham, R.L. and Kozma, S.C. and Thomas, G. and Carling, D. and Okkenhaug, K. and Thornton, Janet M. and Partridge, L. and Gems, D. and Withers, D.J. (2009) Ribosomal protein S6 Kinase 1 signaling regulates mammalian life span. Science 326 (5949), pp. 140-144. ISSN 0036-8075.

Rahman, S.A. and Bashton, M. and Holliday, G.L. and Schrader, R. and Thornton, Janet M. (2009) Small Molecule Subgraph Detector (SMSD) toolkit. Journal of Cheminformatics 1 (1), ISSN 1758-2946.

Cuff, A.I. and Redfern, O.C. and Greene, L. and Sillitoe, I. and Lewis, T.E. and Dibley, M. and Reid, A. and Pearl, F.G.M. and Dallman, T. and Todd, A. and Garratt, R. and Thornton, Janet M. and Orengo, C.A. (2009) The CATH hierarchy revisited - structural divergence in domain superfamilies and the continuity of fold space. Structure 17 (8), pp. 1051-1062. ISSN 0969-2126.

Andreini, C. and Bertini, I. and Cavallaro, G. and Holliday, G.L. and Thornton, Janet M. (2009) Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics 25 (16), pp. 2088-2089. ISSN 1367-4811.

Furnham, N. and Garavelli, J.S. and Apweiler, R. and Thornton, Janet M. (2009) Missing in action: enzyme functional annotations in biological databases. Nature Chemical Biology 5 , pp. 521-525. ISSN 1552-4469.

Laskowski, R.A. and Thornton, Janet M. and Sternberg, M.J.E. (2009) The fine details of evolution. Biochemical Society Transactions 37 , pp. 723-726. ISSN 0300-5127.

Pellegrini-Calace, M. and Maiwald, T. and Thornton, Janet M. (2009) PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Computational Biology 5 (7), ISSN 1553-7358.

Holliday, G.L. and Mitchell, J.B. and Thornton, Janet M. (2009) Understanding the functional roles of amino acid residues in enzyme catalysis. Journal of Molecular Biology 390 (3), pp. 560-577. ISSN 0022-2836.

Laskowski, R.A. and Gerick, F. and Thornton, Janet M. (2009) The structural basis of allosteric regulation in proteins. FEBS Letters 583 (11), pp. 1692-1698. ISSN 1873-3468.

Thornton, Janet M. and Andreini, C. and Bertini, I. and Cavallaro, G. and Najmanovich, R.J. (2009) Structural analysis of metal sites in proteins: non-heme iron sites as a case study. Journal of Molecular Biology 388 (2), pp. 356-380. ISSN 0022-2836.

Talavera, D. and Laskowski, R.A. and Thornton, Janet M. (2009) WSsas: a web service for the annotation of functional residues through structural homologues. Bioinformatics 25 (9), pp. 1192-1194. ISSN 1367-4811.

Persson, B. and Kallberg, Y. and Bray, J.E. and Bruford, E. and Dellaporta, S.L. and Favia, A.D. and Duarte, R.G. and Jörnvall, H. and Kavanagh, K.L. and Kedishvili, N. and Kisiela, M. and Maser, E. and Mindnich, R. and Orchard, S. and Penning, T.M. and Thornton, Janet M. and Adamski, J. and Oppermann, U . (2009) The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chemico-Biological Interactions 178 (1-3), pp. 94-98. ISSN 1872-7786.

Thornton, Janet M. (2009) Annotations for all by all - the BioSapiens network. Genome Biology 10 (2), p. 401. ISSN 1474-7596.

Nobeli, Irene and Favia, A.D. and Thornton, Janet M. (2009) Protein promiscuity and its implications for biotechnology. Nature Biotechnology 27 , pp. 157-167. ISSN 1087-0156.

Reeves, G.A. and Talavera, D. and Thornton, Janet M. (2009) Genome and proteome annotation: organization, interpretation and integration. Journal of the Royal Society - Interface 6 (31), pp. 129-147. ISSN 1742-5689.

Cuff, A.I. and Sillitoe, I. and Lewis, T.E. and Redfern, O.C. and Garratt, R. and Thornton, Janet M. and Orengo, C.A. (2009) The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Research 37 (1(S)), D310-D314. ISSN 0305-1048.

Andreini, C. and Bertini, I. and Cavallaro, G. and Holliday, G.L. and Thornton, Janet M. (2008) Metal ions in biological catalysis: from enzyme databases to general principles. Journal of Biological Inorganic Chemistry 13 (8), pp. 1205-1218. ISSN 0949-8257.

Reeves, G.A. and Eilbeck, K. and Magrane, M. and O'Donovan, C. and Montecchi-Palazzi, L. and Harris, M.A. and Orchard, S. and Jimenez, R.C. and Prlic, A. and Hubbard, T.J. and Hermjakob, H. and Thornton, Janet M. (2008) The protein feature ontology: a tool for the unification of protein feature annotations. Bioinformatics 24 (23), pp. 2767-2772. ISSN 1367-4811.

Freilich, S. and Goldovsky, L. and Ouzounis, C.A. and Thornton, Janet M. (2008) Metabolic innovations towards the human lineage. BMC Evolutionary Biology 8 (247), ISSN 1471-2148.

Najmanovich, R.J. and Kurbatova, N. and Thornton, Janet M. (2008) Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioninformatics 24 (16), i105-i111. ISSN 1367-4803.

Torrance, J.W. and MacArthur, M.W. and Thornton, Janet M. (2008) Evolution of binding sites for Zinc and Calcium ions playing structural roles. Proteins: Structure, Function and Bioinformatics 71 (2), pp. 813-830. ISSN 1097-0134.

Selman, C. and Lingard, S.J. and Choudhury, A.I. and Batterham, R.L. and Claret, M. and Clements, M. and Ramadani, F. and Okkenhaug, K. and Schuster, E. and Blanc, E. and Piper, M.D. and Al-Qassab, H. and Speakman, J.R. and Carmignac, D. and Robinson, I.C.A. and Thornton, Janet M. and Gems, D. and Partridge, L. and Withers, D.J. (2008) Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice. FASEB Journal 22 , pp. 807-818. ISSN 0892-6638.

Laskowski, R.A. and Thornton, Janet M. (2008) Understanding the molecular machinery of genetics through 3D structures. Nature Reviews Genetics 9 (2), pp. 141-151. ISSN 1471-0064.

Favia, A.D. and Nobeli, Irene and Glaser, F. and Thornton, Janet M. (2008) Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. Journal of Molecular Biology 375 (3), pp. 855-874. ISSN 0022-2836.

Bashton, M. and Nobeli, Irene and Thornton, Janet M. (2008) Procognate: a cognate ligand domain mapping for enzymes. Nucleic Acids Research 36 , D618-D622. ISSN 0305-1048.

Pearl, F.M.G. and Bennett, C.F. and Bray, J.E. and Harrison, A.P. and Martin, Nigel and Shepherd, Adrian J. and Sillitoe, I. and Thornton, Janet M. and Orengo, C.A. (2003) The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Research 31 (1), pp. 452-455. ISSN 0305-1048.

Book Section

Watson, J.D. and Thornton, Janet M. (2009) Protein function prediction from structure in structural genomics and its contribution to the study of health and disease. In: Sussman, J.L. and Spadon, P. (eds.) From Molecules to Medicines: Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism. NATO Science for Peace and Security Series A: Chemistry and Biology. Dordrecht, The Netherlands: Springer, pp. 201-215. ISBN 9789048123384.

Kahraman, A. and Thornton, Janet M. (2008) Methods to characterize the structure of enzyme binding sites. In: Schwede, T. and Peitsch, M.C. (eds.) Computational Structural Biology: Methods & Applications Vol. 1. Singapore: World Scientific Pub. Co., pp. 189-221. ISBN 9789812778789.

Nooren, M.A. and Thornton, Janet M. (2004) Molecular sociology. In: Bradshaw, R.A. and Dennis, E.A. (eds.) Handbook of Cell Signaling (2nd ed). California, U.S.: Academic Press Inc., pp. 23-28. ISBN 9780121245474.

Conference or Workshop Item

Thornton, Janet M. and Favia, A.D. and Nobeli, Irene and Furnham, N. (2008) The evolution of specificity in large protein families. In: 33rd FEBS Congress & 11th IUBMB Conference: Biochemistry of Cell Regulation, June 28-July 3 2008, Athens, Greece.