☰

Janet M. Thornton - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 
Area:
protein structures and sequences using computational approaches
Website:
http://www.ebi.ac.uk/about/people/janet-thornton
Tree Info Similar researchers PubMed Report error

410 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Ribeiro AJM, Riziotis IG, Borkakoti N, Thornton JM. Enzyme function and evolution through the lens of bioinformatics. The Biochemical Journal. 480: 1845-1863. PMID 37991346 DOI: 10.1042/BCJ20220405  0.31
2022 Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Lucy Raymond F, Thornton JM. Mapping the Constrained Coding Regions in the human genome to their corresponding proteins. Journal of Molecular Biology. 167892. PMID 36410474 DOI: 10.1016/j.jmb.2022.167892  0.671
2022 Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, ... ... Thornton JM, et al. A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology. PMID 36344848 DOI: 10.1038/s41594-022-00849-w  0.69
2022 Riziotis IG, Thornton JM. Capturing the geometry, function, and evolution of enzymes with 3D templates. Protein Science : a Publication of the Protein Society. 31: e4363. PMID 35762726 DOI: 10.1002/pro.4363  0.355
2022 Riziotis IG, Ribeiro AJM, Borkakoti N, Thornton JM. Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues. Journal of Molecular Biology. 434: 167517. PMID 35240125 DOI: 10.1016/j.jmb.2022.167517  0.325
2021 Laskowski RA, Thornton JM. PDBsum extras: SARS-CoV-2 and AlphaFold models. Protein Science : a Publication of the Protein Society. PMID 34779073 DOI: 10.1002/pro.4238  0.697
2021 Thornton JM, Laskowski RA, Borkakoti N. AlphaFold heralds a data-driven revolution in biology and medicine. Nature Medicine. 27: 1666-1669. PMID 34642488 DOI: 10.1038/s41591-021-01533-0  0.583
2021 Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM. A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. Scientific Reports. 11: 14268. PMID 34253785 DOI: 10.1038/s41598-021-93715-6  0.651
2021 Ochoa R, Laskowski RA, Thornton JM, Cossio P. Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Frontiers in Molecular Biosciences. 8: 636562. PMID 34222328 DOI: 10.3389/fmolb.2021.636562  0.616
2020 Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM. An automated protocol for modelling peptide substrates to proteases. Bmc Bioinformatics. 21: 586. PMID 33375946 DOI: 10.1186/s12859-020-03931-6  0.652
2020 Bjedov I, Cochemé HM, Foley A, Wieser D, Woodling NS, Castillo-Quan JI, Norvaisas P, Lujan C, Regan J, Toivonen JM, Murphy MP, Thornton J, Kinghorn KJ, Neufeld TP, Cabreiro F, et al. Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila. Plos Genetics. 16: e1009083. PMID 33253201 DOI: 10.1371/journal.pgen.1009083  0.595
2020 Dhillon P, Thornton JM. In conversation with Janet Thornton. The Febs Journal. 287: 4106-4113. PMID 33026716 DOI: 10.1111/febs.15567  0.305
2020 Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, ... ... Thornton JM, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000research. 9. PMID 32566135 DOI: 10.12688/F1000Research.20559.1  0.342
2020 Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, Carss KJ, Thornton J, Raymond FL. Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate. Molecular Genetics & Genomic Medicine. e1106. PMID 32347641 DOI: 10.1002/Mgg3.1106  0.319
2019 Ribeiro AJM, Tyzack JD, Borkakoti N, Holliday GL, Thornton JM. A global analysis of function and conservation of catalytic residues in enzymes. The Journal of Biological Chemistry. PMID 31796628 DOI: 10.1074/Jbc.Rev119.006289  0.795
2019 Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM. Identifying pseudoenzymes using functional annotation. How loss of function correlates with mutations in the catalytic site. The Febs Journal. PMID 31733177 DOI: 10.1111/Febs.15142  0.38
2019 Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Exploring Chemical Biosynthetic Design Space with Transform-MinER. Acs Synthetic Biology. PMID 31647630 DOI: 10.1021/Acssynbio.9B00105  0.317
2019 Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA, Thornton JM. VarSite: disease variants and protein structure. Protein Science : a Publication of the Protein Society. PMID 31606900 DOI: 10.1002/Pro.3746  0.706
2019 Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Emerging concepts in pseudoenzyme classification, evolution, and signaling. Science Signaling. 12. PMID 31409758 DOI: 10.1126/Scisignal.Aat9797  0.39
2019 Stephenson JD, Laskowski RA, Nightingale A, Hurles ME, Thornton JM. VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. Bioinformatics (Oxford, England). PMID 31192369 DOI: 10.1093/Bioinformatics/Btz482  0.708
2019 Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S. Finding enzyme cofactors in Protein Data Bank. Bioinformatics (Oxford, England). PMID 30759194 DOI: 10.1093/Bioinformatics/Btz115  0.418
2019 Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function. Methods in Molecular Biology (Clifton, N.J.). 1851: 263-275. PMID 30298402 DOI: 10.1007/978-1-4939-8736-8_14  0.728
2018 Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, Tolulope A, Scholes HM, Senatorov I, Bujan A, Ceballos Rodriguez-Conde F, Dowling B, Thornton J, Orengo CA. CATH: expanding the horizons of structure-based functional annotations for genome sequences. Nucleic Acids Research. PMID 30398663 DOI: 10.1093/Nar/Gky1097  0.401
2018 Tyzack JD, Fernando L, Ribeiro AJM, Borkakoti N, Thornton JM. Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. Structure (London, England : 1993). PMID 29551288 DOI: 10.1016/J.Str.2018.02.009  0.39
2018 Schneider B, Orengo C, Schwede T, Sussman JL, Thornton JM, Velankar S, Wodak S. Coordination of structural bioinformatics activities across Europe Acta Crystallographica Section a Foundations and Advances. 74: e231-e231. DOI: 10.7490/F1000Research.1115607.1  0.329
2017 Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. To what extent do structural changes in catalytic metal sites affect enzyme function? Journal of Inorganic Biochemistry. 179: 40-53. PMID 29161638 DOI: 10.1016/J.Jinorgbio.2017.11.002  0.694
2017 Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Research. PMID 29106569 DOI: 10.1093/Nar/Gkx1012  0.799
2017 Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. Nucleic Acids Research. PMID 29036576 DOI: 10.1093/Nar/Gkx814  0.356
2017 Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, ... Thornton JM, et al. Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1. Molecular Genetics & Genomic Medicine. 5: 495-507. PMID 28944233 DOI: 10.1002/Mgg3.304  0.677
2017 Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Understanding enzyme function evolution from a computational perspective. Current Opinion in Structural Biology. 47: 131-139. PMID 28892668 DOI: 10.1016/J.Sbi.2017.08.003  0.716
2017 Laskowski RA, Jabƚońska J, Pravda L, Vařeková RS, Thornton JM. PDBsum: Structural summaries of PDB entries. Protein Science : a Publication of the Protein Society. PMID 28875543 DOI: 10.1002/Pro.3289  0.712
2017 Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Drug repurposing for aging research using model organisms. Aging Cell. PMID 28620943 DOI: 10.1111/Acel.12626  0.775
2017 Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, ... ... Thornton JM, et al. Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders. Human Molecular Genetics. PMID 28053047 DOI: 10.1093/Hmg/Ddw409  0.651
2016 Mascotti ML, Ayub MJ, Furnham N, Thornton JM, Laskowski RA. Chopping and changing: The evolution of the flavin-dependent monooxygenases. Journal of Molecular Biology. PMID 27423402 DOI: 10.1016/J.Jmb.2016.07.003  0.795
2016 Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinformatics (Oxford, England). PMID 27153692 DOI: 10.1093/Bioinformatics/Btw096  0.773
2016 Martínez Cuesta S, Rahman SA, Thornton JM. Exploring the chemistry and evolution of the isomerases. Proceedings of the National Academy of Sciences of the United States of America. PMID 26842835 DOI: 10.1073/Pnas.1509494113  0.546
2016 Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. Characterising Complex Enzyme Reaction Data. Plos One. 11: e0147952. PMID 26840640 DOI: 10.1371/Journal.Pone.0147952  0.553
2016 Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, Wright CF. Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain. Human Molecular Genetics. PMID 26740553 DOI: 10.1093/Hmg/Ddv625  0.673
2015 Laskowski RA, Thornton JM. Proteins: interaction at a distance. Iucrj. 2: 609-610. PMID 26594367 DOI: 10.1107/S2052252515020217  0.67
2015 Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA. Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. Journal of Molecular Biology. PMID 26585402 DOI: 10.1016/J.Jmb.2015.11.010  0.777
2015 Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N. Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. Plos Computational Biology. 11: e1004546. PMID 26513360 DOI: 10.1371/Journal.Pcbi.1004546  0.691
2015 Hinsley KE, Marshall AC, Hurtig MH, Thornton JM, O'Connell CA, Porter CL, Connor JA, Hickey PA. Monitoring the health of the work environment with a daily assessment tool: the REAL - Relative Environment Assessment Lens - indicator. Cardiology in the Young. 1-8. PMID 26423013 DOI: 10.1017/S1047951115001808  0.403
2015 Sillitoe I, Dawson N, Thornton J, Orengo C. The history of the CATH structural classification of protein domains. Biochimie. PMID 26253692 DOI: 10.1016/J.Biochi.2015.08.004  0.443
2015 Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM. SurvCurv database and online survival analysis platform update. Bioinformatics (Oxford, England). PMID 26249811 DOI: 10.1093/Bioinformatics/Btv463  0.724
2015 Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM. The Classification and Evolution of Enzyme Function. Biophysical Journal. PMID 25986631 DOI: 10.1016/J.Bpj.2015.04.020  0.763
2015 Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM. Longevity GWAS Using the Drosophila Genetic Reference Panel. The Journals of Gerontology. Series a, Biological Sciences and Medical Sciences. PMID 25922346 DOI: 10.1093/Gerona/Glv047  0.73
2015 Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Research. 43: D376-81. PMID 25348408 DOI: 10.1093/Nar/Gku947  0.806
2015 Laskowski RA, Thornton JM. Proteins: Interaction at a distance Iucrj. 2: 609-610. DOI: 10.1107/S2052252515020217  0.63
2015 Thornton J. The Evolution of Enzyme Mechanisms and Functional Diversity Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.211  0.352
2014 Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. The evolution of enzyme function in the isomerases. Current Opinion in Structural Biology. 26: 121-30. PMID 25000289 DOI: 10.1016/J.Sbi.2014.06.002  0.761
2014 Holliday GL, Rahman SA, Furnham N, Thornton JM. Exploring the biological and chemical complexity of the ligases. Journal of Molecular Biology. 426: 2098-111. PMID 24657765 DOI: 10.1016/J.Jmb.2014.03.008  0.811
2014 Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D. MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans. Aging. 6: 98-117. PMID 24531613  0.697
2014 Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D. 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. Plos Genetics. 10: e1004109. PMID 24516399 DOI: 10.1371/Journal.Pgen.1004109  0.552
2014 Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM. EC-BLAST: a tool to automatically search and compare enzyme reactions. Nature Methods. 11: 171-4. PMID 24412978 DOI: 10.1038/Nmeth.2803  0.793
2014 Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Research. 42: D485-9. PMID 24319146 DOI: 10.1093/Nar/Gkt1243  0.816
2014 de Beer TA, Berka K, Thornton JM, Laskowski RA. PDBsum additions. Nucleic Acids Research. 42: D292-6. PMID 24153109 DOI: 10.1093/nar/gkt940  0.765
2013 de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. Plos Computational Biology. 9: e1003382. PMID 24348229 DOI: 10.1371/Journal.Pcbi.1003382  0.773
2013 de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM. LigSearch: a knowledge-based web server to identify likely ligands for a protein target. Acta Crystallographica. Section D, Biological Crystallography. 69: 2395-402. PMID 24311580 DOI: 10.1107/S0907444913022294  0.764
2013 Ziehm M, Thornton JM. Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv. Aging Cell. 12: 910-6. PMID 23826631 DOI: 10.1111/Acel.12121  0.731
2013 Ziehm M, Piper MD, Thornton JM. Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data. Aging Cell. 12: 917-22. PMID 23795998 DOI: 10.1111/Acel.12123  0.721
2013 Li X, Wilmanns M, Thornton J, Köhn M. Elucidating human phosphatase-substrate networks. Science Signaling. 6: rs10. PMID 23674824 DOI: 10.1126/Scisignal.2003203  0.4
2013 Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM. Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster. Molecular Biosystems. 9: 1756-64. PMID 23624434 DOI: 10.1039/C3Mb25485B  0.718
2013 Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Research. 41: D490-8. PMID 23203873 DOI: 10.1093/Nar/Gks1211  0.723
2013 Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, ... ... Thornton JM, et al. The EBI enzyme portal. Nucleic Acids Research. 41: D773-80. PMID 23175605 DOI: 10.1093/Nar/Gks1112  0.809
2013 Furnham N, Laskowski RA, Thornton JM. Abstracting knowledge from the protein data bank. Biopolymers. 99: 183-8. PMID 23023892 DOI: 10.1002/Bip.22107  0.811
2012 Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM. Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing. Plos One. 7: e50881. PMID 23251396 DOI: 10.1371/Journal.Pone.0050881  0.778
2012 Furnham N, de Beer TA, Thornton JM. Current challenges in genome annotation through structural biology and bioinformatics. Current Opinion in Structural Biology. 22: 594-601. PMID 22884875 DOI: 10.1016/J.Sbi.2012.07.005  0.769
2012 Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM. Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. Plos Computational Biology. 8: e1002403. PMID 22396634 DOI: 10.1371/Journal.Pcbi.1002403  0.817
2012 Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM. FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Research. 40: D776-82. PMID 22006843 DOI: 10.1093/Nar/Gkr852  0.82
2012 Cuesta SM, Furnham N, Thornton JM. Evolution of NAD (P)H binding domain superfamily F1000research. 3. DOI: 10.7490/F1000Research.1089820.1  0.647
2012 Orengo C, Thornton J. Protein‐fold classification International Tables For Crystallography. DOI: 10.1107/97809553602060000890  0.393
2012 Laskowski RA, MacArthur MW, Thornton JM. PROCHECK: validation of protein‐structure coordinates International Tables For Crystallography. 684-687. DOI: 10.1107/97809553602060000882  0.315
2011 McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P, Köhn M. The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides. Biochemistry. 50: 7579-90. PMID 21806020 DOI: 10.1021/Bi201095Z  0.336
2011 Alic N, Andrews TD, Giannakou ME, Papatheodorou I, Slack C, Hoddinott MP, Cochemé HM, Schuster EF, Thornton JM, Partridge L. Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling. Molecular Systems Biology. 7: 502. PMID 21694719 DOI: 10.1038/Msb.2011.36  0.522
2011 Holliday GL, Fischer JD, Mitchell JB, Thornton JM. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. The Febs Journal. 278: 3835-45. PMID 21605342 DOI: 10.1111/J.1742-4658.2011.08190.X  0.815
2011 Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA. 1,000 structures and more from the MCSG. Bmc Structural Biology. 11: 2. PMID 21219649 DOI: 10.1186/1472-6807-11-2  0.773
2011 Wieser D, Papatheodorou I, Ziehm M, Thornton JM. Computational biology for ageing. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 366: 51-63. PMID 21115530 DOI: 10.1098/Rstb.2010.0286  0.778
2011 Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA. Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Research. 39: D420-6. PMID 21097779 DOI: 10.1093/Nar/Gkq1001  0.83
2011 Rahman SA, Torrence G, Fenninger F, Baldacci L, Gopal N, Holliday GL, Thornton JM. Automated analysis of enzyme reaction mechanisms F1000research. 2. DOI: 10.7490/F1000Research.2088.1  0.525
2010 Fischer JD, Holliday GL, Rahman SA, Thornton JM. The structures and physicochemical properties of organic cofactors in biocatalysis. Journal of Molecular Biology. 403: 803-24. PMID 20850456 DOI: 10.1016/J.Jmb.2010.09.018  0.809
2010 Schuster E, McElwee JJ, Tullet JM, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D. DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO. Molecular Systems Biology. 6: 399. PMID 20706209 DOI: 10.1038/Msb.2010.54  0.52
2010 Fischer JD, Holliday GL, Thornton JM. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics (Oxford, England). 26: 2496-7. PMID 20679331 DOI: 10.1093/Bioinformatics/Btq442  0.8
2010 Smith LJ, Kahraman A, Thornton JM. Heme proteins--diversity in structural characteristics, function, and folding. Proteins. 78: 2349-68. PMID 20544970 DOI: 10.1002/Prot.22747  0.614
2010 Slack C, Werz C, Wieser D, Alic N, Foley A, Stocker H, Withers DJ, Thornton JM, Hafen E, Partridge L. Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk. Plos Genetics. 6: e1000881. PMID 20333234 DOI: 10.1371/Journal.Pgen.1000881  0.684
2010 Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M. 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: 4135-40. PMID 20147624 DOI: 10.1073/Pnas.0910632107  0.753
2010 Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM. On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins. 78: 1120-36. PMID 19927322 DOI: 10.1002/Prot.22633  0.769
2010 Bashton M, Thornton JM. Domain-ligand mapping for enzymes. Journal of Molecular Recognition : Jmr. 23: 194-208. PMID 19810051 DOI: 10.1002/Jmr.992  0.716
2010 Talavera D, Taylor MS, Thornton JM. The (non)malignancy of cancerous amino acidic substitutions. Proteins. 78: 518-29. PMID 19787769 DOI: 10.1002/Prot.22574  0.615
2009 Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Small Molecule Subgraph Detector (SMSD) toolkit. Journal of Cheminformatics. 1: 12. PMID 20298518 DOI: 10.1186/1758-2946-1-12  0.784
2009 Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Plos Computational Biology. 5: e1000585. PMID 19997483 DOI: 10.1371/Journal.Pcbi.1000585  0.721
2009 Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M, Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, ... ... Thornton JM, et al. Ribosomal protein S6 kinase 1 signaling regulates mammalian life span. Science (New York, N.Y.). 326: 140-4. PMID 19797661 DOI: 10.1126/Science.1177221  0.719
2009 Macchiarulo A, Thornton JM, Nobeli I. Mapping human metabolic pathways in the small molecule chemical space. Journal of Chemical Information and Modeling. 49: 2272-89. PMID 19795883 DOI: 10.1021/Ci900196U  0.748
2009 Oliva R, Thornton JM, Pellegrini-Calace M. PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins. Bioinformatics (Oxford, England). 25: 3183-4. PMID 19762348 DOI: 10.1093/Bioinformatics/Btp545  0.783
2009 Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C. The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure (London, England : 1993). 17: 1051-62. PMID 19679085 DOI: 10.1016/J.Str.2009.06.015  0.624
2009 Furnham N, Garavelli JS, Apweiler R, Thornton JM. Missing in action: enzyme functional annotations in biological databases. Nature Chemical Biology. 5: 521-5. PMID 19620987 DOI: 10.1038/Nchembio0809-521  0.704
2009 Laskowski RA, Thornton JM, Sternberg MJ. The fine details of evolution. Biochemical Society Transactions. 37: 723-6. PMID 19614583 DOI: 10.1042/Bst0370723  0.75
2009 Pellegrini-Calace M, Maiwald T, Thornton JM. PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. Plos Computational Biology. 5: e1000440. PMID 19609355 DOI: 10.1371/Journal.Pcbi.1000440  0.769
2009 Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. Journal of Molecular Biology. 390: 560-77. PMID 19447117 DOI: 10.1016/J.Jmb.2009.05.015  0.807
2009 Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics (Oxford, England). 25: 2088-9. PMID 19369503 DOI: 10.1093/Bioinformatics/Btp256  0.729
2009 Laskowski RA, Gerick F, Thornton JM. The structural basis of allosteric regulation in proteins. Febs Letters. 583: 1692-8. PMID 19303011 DOI: 10.1016/J.Febslet.2009.03.019  0.816
2009 Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. Journal of Molecular Biology. 388: 356-80. PMID 19265704 DOI: 10.1016/J.Jmb.2009.02.052  0.706
2009 Talavera D, Laskowski RA, Thornton JM. WSsas: a web service for the annotation of functional residues through structural homologues. Bioinformatics (Oxford, England). 25: 1192-4. PMID 19251774 DOI: 10.1093/Bioinformatics/Btp116  0.796
2009 Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A. Protein function annotation by homology-based inference. Genome Biology. 10: 207. PMID 19226439 DOI: 10.1186/Gb-2009-10-2-207  0.55
2009 Nobeli I, Favia AD, Thornton JM. Protein promiscuity and its implications for biotechnology. Nature Biotechnology. 27: 157-67. PMID 19204698 DOI: 10.1038/Nbt1519  0.737
2009 Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, ... Thornton JM, et al. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chemico-Biological Interactions. 178: 94-8. PMID 19027726 DOI: 10.1016/J.Cbi.2008.10.040  0.389
2009 Reeves GA, Talavera D, Thornton JM. Genome and proteome annotation: organization, interpretation and integration. Journal of the Royal Society, Interface / the Royal Society. 6: 129-47. PMID 19019817 DOI: 10.1098/Rsif.2008.0341  0.717
2009 Cuff AI, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA. The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies Nucleic Acids Research. 37: D310-D314. PMID 18996897 DOI: 10.1093/Nar/Gkn877  0.632
2009 Watson JD, Thornton JM. Protein function prediction from structure in structural genomics and its contribution to the study of health and disease Nato Science For Peace and Security Series a: Chemistry and Biology. 201-215. DOI: 10.1007/978-90-481-2339-1-13  0.456
2009 Watson JD, Thornton JM. Case studies: Function predictions of structural genomics results From Protein Structure to Function With Bioinformatics. 273-291. DOI: 10.1007/978-1-4020-9058-5_11  0.405
2009 Watson JD, Thornton JM. Protein function prediction from structure in structural genomics and its contribution to the study of health and disease Nato Science For Peace and Security Series a: Chemistry and Biology. 201-215.  0.456
2009 Sternberg M, Thornton J, Laskowski R. Protein evolution - Sequence, structure and systems Biochemist. 31: 52-52.  0.661
2008 Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (Oxford, England). 24: 2767-72. PMID 18936051 DOI: 10.1093/Bioinformatics/Btn528  0.628
2008 Freilich S, Goldovsky L, Ouzounis CA, Thornton JM. Metabolic innovations towards the human lineage. Bmc Evolutionary Biology. 8: 247. PMID 18782449 DOI: 10.1186/1471-2148-8-247  0.622
2008 Najmanovich R, Kurbatova N, Thornton J. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites Bioinformatics. 24: i105-i111. PMID 18689810 DOI: 10.1093/bioinformatics/btn263  0.685
2008 Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 13: 1205-18. PMID 18604568 DOI: 10.1007/S00775-008-0404-5  0.743
2008 Laskowski RA, Thornton JM. Understanding the molecular machinery of genetics through 3D structures. Nature Reviews. Genetics. 9: 141-51. PMID 18160966 DOI: 10.1038/Nrg2273  0.7
2008 Favia AD, Nobeli I, Glaser F, Thornton JM. Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. Journal of Molecular Biology. 375: 855-74. PMID 18036612 DOI: 10.1016/J.Jmb.2007.10.065  0.805
2008 Torrance JW, Macarthur MW, Thornton JM. Evolution of binding sites for zinc and calcium ions playing structural roles. Proteins. 71: 813-30. PMID 18004751 DOI: 10.1002/Prot.21741  0.742
2008 Selman C, Lingard S, Choudhury AI, Batterham RL, Claret M, Clements M, Ramadani F, Okkenhaug K, Schuster E, Blanc E, Piper MD, Al-Qassab H, Speakman JR, Carmignac D, Robinson IC, ... Thornton JM, et al. Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 22: 807-18. PMID 17928362 DOI: 10.1096/Fj.07-9261Com  0.631
2008 Bashton M, Nobeli I, Thornton JM. PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Research. 36: D618-22. PMID 17720712 DOI: 10.1093/Nar/Gkm611  0.817
2008 Tress ML, Casadio R, Giorgetti A, Hallin PF, Juncker AS, Kulberkyte E, Martelli P, Raimondo D, Reeves GA, Thornton JM, Tramontano A, Wang K, Wesselink JJ, Valencia A. Alternative splicing in the ENCODE protein complement Modern Genome Annotation: the Biosapiens Network. 453-484. DOI: 10.1007/978-3-211-75123-7_20  0.522
2008 Watson JD, Thornton JM, Tress ML, Lopez G, Valencia A, Redfern O, Orengo CA, Sommer I, Domingues FS. Structure to function Modern Genome Annotation: the Biosapiens Network. 239-262. DOI: 10.1007/978-3-211-75123-7_12  0.426
2008 Torrance JW, Thornton JM. Structure-Based Prediction of Enzymes and Their Active Sites Prediction of Protein Structures, Functions, and Interactions. 187-209. DOI: 10.1002/9780470741894.ch8  0.526
2007 Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ. Construction, visualisation, and clustering of transcription networks from microarray expression data. Plos Computational Biology. 3: 2032-42. PMID 17967053 DOI: 10.1371/Journal.Pcbi.0030206  0.617
2007 Ward JJ, Thornton JM. Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network. Plos Computational Biology. 3: 1993-2002. PMID 17967049 DOI: 10.1371/Journal.Pcbi.0030198  0.495
2007 Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ. Evolution of enzymes and pathways for the biosynthesis of cofactors. Natural Product Reports. 24: 972-87. PMID 17898893 DOI: 10.1039/B703107F  0.758
2007 Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. The chemistry of protein catalysis. Journal of Molecular Biology. 372: 1261-77. PMID 17727879 DOI: 10.1016/J.Jmb.2007.07.034  0.804
2007 McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas JH, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D. Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biology. 8: R132. PMID 17612391 DOI: 10.1186/Gb-2007-8-7-R132  0.663
2007 Schuster EF, Blanc E, Partridge L, Thornton JM. Estimation and correction of non-specific binding in a large-scale spike-in experiment. Genome Biology. 8: R126. PMID 17594493 DOI: 10.1186/Gb-2007-8-6-R126  0.661
2007 Schuster EF, Blanc E, Partridge L, Thornton JM. Correcting for sequence biases in present/absent calls. Genome Biology. 8: R125. PMID 17594492 DOI: 10.1186/Gb-2007-8-6-R125  0.66
2007 Torrance JW, Holliday GL, Mitchell JB, Thornton JM. The geometry of interactions between catalytic residues and their substrates. Journal of Molecular Biology. 369: 1140-52. PMID 17466330 DOI: 10.1016/J.Jmb.2007.03.055  0.814
2007 Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Thonton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. Structural and chemical profiling of the human cytosolic sulfotransferases. Plos Biology. 5: e97. PMID 17425406 DOI: 10.1371/journal.pbio.0050097  0.683
2007 Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, ... ... Thornton JM, et al. The implications of alternative splicing in the ENCODE protein complement. Proceedings of the National Academy of Sciences of the United States of America. 104: 5495-500. PMID 17372197 DOI: 10.1073/Pnas.0700800104  0.769
2007 Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Shape variation in protein binding pockets and their ligands. Journal of Molecular Biology. 368: 283-301. PMID 17337005 DOI: 10.1016/J.Jmb.2007.01.086  0.752
2007 Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM. Towards fully automated structure-based function prediction in structural genomics: a case study. Journal of Molecular Biology. 367: 1511-22. PMID 17316683 DOI: 10.1016/J.Jmb.2007.01.063  0.755
2007 Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM. Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. Bioinformatics (Oxford, England). 23: e104-9. PMID 17237076 DOI: 10.1093/Bioinformatics/Btl292  0.72
2007 Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Research. 35: D291-7. PMID 17135200 DOI: 10.1093/Nar/Gkl959  0.4
2007 Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Research. 35: D515-20. PMID 17082206 DOI: 10.1093/Nar/Gkl774  0.79
2007 Allali-Hassani A, Pan W, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards A, Bochkarev A, Plotnikov A, Vedadi M, Arrowsmith C. Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases Plos Biology. 5: e165. DOI: 10.1371/Journal.Pbio.0050165  0.308
2007 Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Variation of geometrical and physicochemical properties in protein binding pockets and their ligands Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-S1  0.75
2006 McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D. 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]. Mechanisms of Ageing and Development. 127: 922-36. PMID 17216712 DOI: 10.1016/J.Mad.2006.10.002  0.641
2006 Bashton M, Nobeli I, Thornton JM. Cognate ligand domain mapping for enzymes. Journal of Molecular Biology. 364: 836-52. PMID 17034815 DOI: 10.1016/J.Jmb.2006.09.041  0.801
2006 Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM. Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. Genome Biology. 7: R89. PMID 17029626 DOI: 10.1186/Gb-2006-7-10-R89  0.768
2006 Ranea JA, Sillero A, Thornton JM, Orengo CA. Protein superfamily evolution and the last universal common ancestor (LUCA). Journal of Molecular Evolution. 63: 513-25. PMID 17021929 DOI: 10.1007/S00239-005-0289-7  0.386
2006 Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, ... ... Thornton JM, et al. SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallographica. Section D, Biological Crystallography. 62: 1184-95. PMID 17001095 DOI: 10.1107/S090744490602991X  0.777
2006 Selman C, Kerrison ND, Cooray A, Piper MD, Lingard SJ, Barton RH, Schuster EF, Blanc E, Gems D, Nicholson JK, Thornton JM, Partridge L, Withers DJ. Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice. Physiological Genomics. 27: 187-200. PMID 16882887 DOI: 10.1152/Physiolgenomics.00084.2006  0.77
2006 Reeves GA, Thornton JM. Integrating biological data through the genome. Human Molecular Genetics. 15: R81-7. PMID 16651373 DOI: 10.1093/Hmg/Ddl086  0.575
2006 Whamond GS, Thornton JM. An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure. Journal of Molecular Biology. 359: 238-47. PMID 16616935 DOI: 10.1016/J.Jmb.2006.03.029  0.801
2006 Nobeli I, Thornton JM. A bioinformatician's view of the metabolome. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 28: 534-45. PMID 16615085 DOI: 10.1002/Bies.20414  0.708
2006 Jones DT, Sternberg MJ, Thornton JM. Introduction. Bioinformatics: from molecules to systems. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 389-91. PMID 16524827 DOI: 10.1098/Rstb.2005.1811  0.578
2006 McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D. Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans. Mechanisms of Ageing and Development. 127: 458-72. PMID 16522328 DOI: 10.1016/J.Mad.2006.01.006  0.641
2006 Stockwell GR, Thornton JM. Conformational diversity of ligands bound to proteins. Journal of Molecular Biology. 356: 928-44. PMID 16405908 DOI: 10.1016/J.Jmb.2005.12.012  0.778
2006 Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM. A method for localizing ligand binding pockets in protein structures. Proteins. 62: 479-88. PMID 16304646 DOI: 10.1002/Prot.20769  0.811
2006 Furey W, Cowtan KD, Zhang KYJ, Main P, Brunger AT, Adams PD, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-, Pannu NS, Read RJ, Rice LM, Simonson T, Tronrud DE, ... ... Thornton JM, et al. Programs and program systems in wide use International Tables For Crystallography. 695-743. DOI: 10.1107/97809553602060000724  0.301
2005 Gutteridge A, Thornton JM. Understanding nature's catalytic toolkit. Trends in Biochemical Sciences. 30: 622-9. PMID 16214343 DOI: 10.1016/J.Tibs.2005.09.006  0.713
2005 Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. MACiE: a database of enzyme reaction mechanisms. Bioinformatics (Oxford, England). 21: 4315-6. PMID 16188925 DOI: 10.1093/Bioinformatics/Bti693  0.787
2005 George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB. Effective function annotation through catalytic residue conservation. Proceedings of the National Academy of Sciences of the United States of America. 102: 12299-304. PMID 16037208 DOI: 10.1073/Pnas.0504833102  0.822
2005 Ferrer-Costa C, Shanahan HP, Jones S, Thornton JM. HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif. Bioinformatics (Oxford, England). 21: 3679-80. PMID 16030074 DOI: 10.1093/Bioinformatics/Bti575  0.767
2005 Laskowski RA, Watson JD, Thornton JM. Protein function prediction using local 3D templates. Journal of Molecular Biology. 351: 614-26. PMID 16019027 DOI: 10.1016/J.Jmb.2005.05.067  0.757
2005 Najmanovich RJ, Torrance JW, Thornton JM. Prediction of protein function from structure: insights from methods for the detection of local structural similarities. Biotechniques. 38: 847, 849, 851. PMID 16018542 DOI: 10.2144/05386Te01  0.762
2005 Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM. Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biology. 6: R56. PMID 15998445 DOI: 10.1186/Gb-2005-6-7-R56  0.807
2005 Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Research. 33: W89-93. PMID 15980588 DOI: 10.1093/Nar/Gki414  0.764
2005 Watson JD, Laskowski RA, Thornton JM. Predicting protein function from sequence and structural data. Current Opinion in Structural Biology. 15: 275-84. PMID 15963890 DOI: 10.1016/J.Sbi.2005.04.003  0.75
2005 Orengo CA, Thornton JM. Protein families and their evolution-a structural perspective. Annual Review of Biochemistry. 74: 867-900. PMID 15954844 DOI: 10.1146/Annurev.Biochem.74.082803.133029  0.365
2005 Shanahan HP, Thornton JM. Amino acid architecture and the distribution of polar atoms on the surfaces of proteins. Biopolymers. 78: 318-28. PMID 15898105 DOI: 10.1002/Bip.20295  0.624
2005 Freilich S, Spriggs RV, George RA, Al-Lazikani B, Swindells M, Thornton JM. The complement of enzymatic sets in different species. Journal of Molecular Biology. 349: 745-63. PMID 15896806 DOI: 10.1016/J.Jmb.2005.04.027  0.805
2005 Ponstingl H, Kabir T, Gorse D, Thornton JM. Morphological aspects of oligomeric protein structures. Progress in Biophysics and Molecular Biology. 89: 9-35. PMID 15895504 DOI: 10.1016/J.Pbiomolbio.2004.07.010  0.668
2005 Todd AE, Marsden RL, Thornton JM, Orengo CA. Progress of structural genomics initiatives: an analysis of solved target structures. Journal of Molecular Biology. 348: 1235-60. PMID 15854658 DOI: 10.1016/J.Jmb.2005.03.037  0.429
2005 Pellegrini-Calace M, Thornton JM. Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information. Nucleic Acids Research. 33: 2129-40. PMID 15831786 DOI: 10.1093/Nar/Gki349  0.796
2005 Torrance JW, Bartlett GJ, Porter CT, Thornton JM. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. Journal of Molecular Biology. 347: 565-81. PMID 15755451 DOI: 10.1016/J.Jmb.2005.01.044  0.73
2005 Nobeli I, Spriggs RV, George RA, Thornton JM. A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli. Journal of Molecular Biology. 347: 415-36. PMID 15740750 DOI: 10.1016/J.Jmb.2005.01.061  0.837
2005 Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics (Oxford, England). 21: 2347-55. PMID 15728116 DOI: 10.1093/Bioinformatics/Bti337  0.802
2005 Gutteridge A, Thornton J. Conformational changes observed in enzyme crystal structures upon substrate binding. Journal of Molecular Biology. 346: 21-8. PMID 15663924 DOI: 10.1016/J.Jmb.2004.11.013  0.711
2005 Brooksbank C, Cameron G, Thornton J. The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Research. 33: D46-53. PMID 15608238 DOI: 10.1093/Nar/Gki026  0.304
2005 Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Research. 33: D266-8. PMID 15608193 DOI: 10.1093/Nar/Gki001  0.7
2005 Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, ... ... Thornton J, et al. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Research. 33: D247-51. PMID 15608188 DOI: 10.1093/Nar/Gki024  0.604
2005 Kerrison ND, Selman C, Lingard SJ, Thornton JM, Partridge L, Withers DJ. Living longer by dieting: analysis of transcriptional response after caloric restriction Bmc Bioinformatics. 6: S6. DOI: 10.1186/1471-2105-6-S3-S6  0.669
2005 Morris RJ, Kahraman A, Thornton JM. Binding pocket shape analysis for protein function prediction Acta Crystallographica Section a Foundations of Crystallography. 61: c156-c157. DOI: 10.1107/S0108767305093347  0.647
2005 Joachimiak A, Zhang R, Kim Y, Osipiuk J, Cuff M, Chang C, Nocek B, Binkowski A, Cymborowski M, Lazarski K, Chruszcz M, Laskowski R, Thornton J, Duke N, Rotella F, et al. Establishing high-throughput protein structure determination pipeline for structural genomics Acta Crystallographica Section a Foundations of Crystallography. 61: c259-c259. DOI: 10.1107/S0108767305088926  0.695
2005 Todd AE, Marsden RL, Thornton JM, Orengo CA. Corrigendum to “Progress of Structural Genomics Initiatives: An Analysis of Solved Target Structures” [J. Mol. Biol. (2005) 348, 1235–1260] Journal of Molecular Biology. 353: 760. DOI: 10.1016/J.Jmb.2005.09.001  0.302
2004 Eyre TA, Partridge L, Thornton JM. Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models. Protein Engineering, Design & Selection : Peds. 17: 613-24. PMID 15388845 DOI: 10.1093/Protein/Gzh072  0.384
2004 Shanahan HP, Garcia MA, Jones S, Thornton JM. Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Research. 32: 4732-41. PMID 15356290 DOI: 10.1093/Nar/Gkh803  0.771
2004 Murray KB, Taylor WR, Thornton JM. Toward the detection and validation of repeats in protein structure. Proteins. 57: 365-80. PMID 15340924 DOI: 10.1002/Prot.20202  0.537
2004 Macchiarulo A, Nobeli I, Thornton JM. Ligand selectivity and competition between enzymes in silico. Nature Biotechnology. 22: 1039-45. PMID 15286657 DOI: 10.1038/Nbt999  0.798
2004 George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB. SCOPEC: a database of protein catalytic domains. Bioinformatics (Oxford, England). 20: i130-6. PMID 15262791 DOI: 10.1093/bioinformatics/bth948  0.813
2004 Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA. A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics (Oxford, England). 20: 2288-95. PMID 15201178 DOI: 10.1093/Bioinformatics/Bth240  0.357
2004 Gutteridge A, Thornton J. Conformational change in substrate binding, catalysis and product release: an open and shut case? Febs Letters. 567: 67-73. PMID 15165895 DOI: 10.1016/J.Febslet.2004.03.067  0.697
2004 Ranea JA, Buchan DW, Thornton JM, Orengo CA. Evolution of protein superfamilies and bacterial genome size. Journal of Molecular Biology. 336: 871-87. PMID 15095866 DOI: 10.1016/J.Jmb.2003.12.044  0.318
2004 Shanahan HP, Thornton JM. An examination of the conservation of surface patch polarity for proteins. Bioinformatics (Oxford, England). 20: 2197-204. PMID 15073014 DOI: 10.1093/Bioinformatics/Bth218  0.651
2004 Jones S, Thornton JM. Searching for functional sites in protein structures. Current Opinion in Chemical Biology. 8: 3-7. PMID 15036149 DOI: 10.1016/J.Cbpa.2003.11.001  0.687
2004 Porter CT, Bartlett GJ, Thornton JM. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Research. 32: D129-33. PMID 14681376 DOI: 10.1093/Nar/Gkh028  0.611
2004 Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C. Recognizing the fold of a protein structure. Bioinformatics (Oxford, England). 19: 1748-59. PMID 14512345 DOI: 10.1093/Bioinformatics/Btg240  0.425
2003 Jones S, Thornton JM. Protein-DNA interactions: the story so far and a new method for prediction. Comparative and Functional Genomics. 4: 428-31. PMID 18629075 DOI: 10.1002/Cfg.303  0.666
2003 Jones S, Shanahan HP, Berman HM, Thornton JM. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Research. 31: 7189-98. PMID 14654694 DOI: 10.1093/Nar/Gkg922  0.744
2003 Laskowski RA, Watson JD, Thornton JM. From protein structure to biochemical function? Journal of Structural and Functional Genomics. 4: 167-77. PMID 14649301 DOI: 10.1023/A:1026127927612  0.748
2003 Nobeli I, Ponstingl H, Krissinel EB, Thornton JM. A structure-based anatomy of the E.coli metabolome. Journal of Molecular Biology. 334: 697-719. PMID 14636597 DOI: 10.1016/J.Jmb.2003.10.008  0.799
2003 Barker JA, Thornton JM. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics (Oxford, England). 19: 1644-9. PMID 12967960 DOI: 10.1093/Bioinformatics/Btg226  0.395
2003 Steward RE, MacArthur MW, Laskowski RA, Thornton JM. Molecular basis of inherited diseases: a structural perspective. Trends in Genetics : Tig. 19: 505-13. PMID 12957544 DOI: 10.1016/S0168-9525(03)00195-1  0.808
2003 Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG. Analysis of metabolic networks using a pathway distance metric through linear programming. Metabolic Engineering. 5: 211-9. PMID 12948755 DOI: 10.1016/S1096-7176(03)00043-0  0.315
2003 Bartlett GJ, Borkakoti N, Thornton JM. Catalysing new reactions during evolution: economy of residues and mechanism. Journal of Molecular Biology. 331: 829-60. PMID 12909013 DOI: 10.1016/S0022-2836(03)00734-4  0.417
2003 Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM. Target selection and determination of function in structural genomics. Iubmb Life. 55: 249-55. PMID 12880206 DOI: 10.1080/1521654031000123385  0.75
2003 Dawe JH, Porter CT, Thornton JM, Tabor AB. A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes. Proteins. 52: 427-35. PMID 12866053 DOI: 10.1002/Prot.10421  0.59
2003 Nooren IM, Thornton JM. Diversity of protein-protein interactions. The Embo Journal. 22: 3486-92. PMID 12853464 DOI: 10.1093/Emboj/Cdg359  0.417
2003 Gutteridge A, Bartlett GJ, Thornton JM. Using a neural network and spatial clustering to predict the location of active sites in enzymes. Journal of Molecular Biology. 330: 719-34. PMID 12850142 DOI: 10.1016/S0022-2836(03)00515-1  0.707
2003 Jones S, Barker JA, Nobeli I, Thornton JM. Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Research. 31: 2811-23. PMID 12771208 DOI: 10.1093/Nar/Gkg386  0.81
2003 Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. The Journal of Biological Chemistry. 278: 26039-45. PMID 12732651 DOI: 10.1074/Jbc.M303867200  0.72
2003 Bartlett GJ, Todd AE, Thornton JM. Inferring protein function from structure. Methods of Biochemical Analysis. 44: 387-407. PMID 12647396 DOI: 10.1002/0471721204.Ch19  0.428
2003 Orengo CA, Pearl FM, Thornton JM. The CATH domain structure database. Methods of Biochemical Analysis. 44: 249-71. PMID 12647390 DOI: 10.1002/0471721204.Ch13  0.332
2003 Nooren IM, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. Journal of Molecular Biology. 325: 991-1018. PMID 12527304 DOI: 10.1016/S0022-2836(02)01281-0  0.394
2003 Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Research. 31: 469-73. PMID 12520054 DOI: 10.1093/Nar/Gkg051  0.389
2003 Pearl FMG, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA. The CATH database: An extended protein family resource for structural and functional genomics Nucleic Acids Research. 31: 452-455. PMID 12520050 DOI: 10.1093/Nar/Gkg062  0.387
2003 Shepherd AJ, Gorse D, Thornton JM. A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks. Proteins. 50: 290-302. PMID 12486723 DOI: 10.1002/Prot.10290  0.349
2003 Ponstingl H, Kabir T, Thornton JM. Automatic inference of protein quaternary structure from crystals Journal of Applied Crystallography. 36: 1116-1122. DOI: 10.1107/S0021889803012421  0.664
2002 Bartlett GJ, Porter CT, Borkakoti N, Thornton JM. Analysis of catalytic residues in enzyme active sites. Journal of Molecular Biology. 324: 105-21. PMID 12421562 DOI: 10.1016/S0022-2836(02)01036-7  0.614
2002 Harrison A, Pearl F, Mott R, Thornton J, Orengo C. Quantifying the similarities within fold space. Journal of Molecular Biology. 323: 909-26. PMID 12417203 DOI: 10.1016/S0022-2836(02)00992-0  0.348
2002 Todd AE, Orengo CA, Thornton JM. Sequence and structural differences between enzyme and nonenzyme homologs. Structure (London, England : 1993). 10: 1435-51. PMID 12377129 DOI: 10.1016/S0969-2126(02)00861-4  0.417
2002 Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. Journal of Molecular Biology. 321: 741-65. PMID 12206759 DOI: 10.1016/S0022-2836(02)00649-6  0.462
2002 de la Cruz X, Hutchinson EG, Shepherd A, Thornton JM. Toward predicting protein topology: an approach to identifying beta hairpins. Proceedings of the National Academy of Sciences of the United States of America. 99: 11157-62. PMID 12177429 DOI: 10.1073/Pnas.162376199  0.34
2002 Todd AE, Orengo CA, Thornton JM. Plasticity of enzyme active sites. Trends in Biochemical Sciences. 27: 419-26. PMID 12151227 DOI: 10.1016/S0968-0004(02)02158-8  0.369
2002 Rison SC, Thornton JM. Pathway evolution, structurally speaking. Current Opinion in Structural Biology. 12: 374-82. PMID 12127458 DOI: 10.1016/S0959-440X(02)00331-7  0.362
2002 Luscombe NM, Thornton JM. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. Journal of Molecular Biology. 320: 991-1009. PMID 12126620 DOI: 10.1016/S0022-2836(02)00571-5  0.363
2002 Steward RE, Thornton JM. Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins. 48: 178-91. PMID 12112687 DOI: 10.1002/Prot.10152  0.538
2002 Rison SC, Teichmann SA, Thornton JM. Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. Journal of Molecular Biology. 318: 911-32. PMID 12054833 DOI: 10.1016/S0022-2836(02)00140-7  0.557
2002 Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA. Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Research. 12: 503-14. PMID 11875040 DOI: 10.1101/Gr.213802  0.39
2002 Murray KB, Gorse D, Thornton JM. Wavelet transforms for the characterization and detection of repeating motifs. Journal of Molecular Biology. 316: 341-63. PMID 11851343 DOI: 10.1006/Jmbi.2001.5332  0.555
2002 Martin AC, Facchiano AM, Cuff AL, Hernandez-Boussard T, Olivier M, Hainaut P, Thornton JM. Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein. Human Mutation. 19: 149-64. PMID 11793474 DOI: 10.1002/Humu.10032  0.343
2002 Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM. The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics. 2: 11-21. PMID 11788987 DOI: 10.1002/1615-9861(200201)2:1<11::Aid-Prot11>3.0.Co;2-T  0.444
2002 Gilbert D, Westhead D, Viksna J, Thornton J. A computer system to perform structure comparison using TOPS representations of protein structure. Computers & Chemistry. 26: 23-30. PMID 11765848 DOI: 10.1016/S0097-8485(01)00096-1  0.439
2002 Thornton J, Laskowski RA, Bartlett G, Porter C, Todd A, Orengo C. Enzymes: evolution of function from a structural perspective Acta Crystallographica Section a Foundations of Crystallography. 58: c13-c13. DOI: 10.1107/S0108767302085616  0.752
2001 Nagano N, Porter CT, Thornton JM. The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships. Protein Engineering. 14: 845-55. PMID 11742103 DOI: 10.1093/Protein/14.11.845  0.553
2001 Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C. Small-molecule metabolism: an enzyme mosaic. Trends in Biotechnology. 19: 482-6. PMID 11711174 DOI: 10.1016/S0167-7799(01)01813-3  0.692
2001 Nobeli I, Laskowski RA, Valdar WS, Thornton JM. On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Research. 29: 4294-309. PMID 11691917 DOI: 10.1093/Nar/29.21.4294  0.819
2001 Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. Journal of Molecular Biology. 311: 693-708. PMID 11518524 DOI: 10.1006/Jmbi.2001.4912  0.707
2001 Luscombe NM, Laskowski RA, Thornton JM. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Research. 29: 2860-74. PMID 11433033 DOI: 10.1093/Nar/29.13.2860  0.663
2001 Thornton JM. From genome to function. Science (New York, N.Y.). 292: 2095-7. PMID 11408660 DOI: 10.1126/Science.292.5524.2095  0.4
2001 Thornton J. Structural genomics takes off. Trends in Biochemical Sciences. 26: 88-9. PMID 11327043 DOI: 10.1016/S0968-0004(00)01765-5  0.315
2001 Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology. 307: 1113-43. PMID 11286560 DOI: 10.1006/Jmbi.2001.4513  0.485
2001 Thornton JM. The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution. Protein Science : a Publication of the Protein Society. 10: 3-11. PMID 11266588 DOI: 10.1110/Ps.90001  0.429
2001 Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM. Protein-RNA interactions: a structural analysis. Nucleic Acids Research. 29: 943-54. PMID 11160927 DOI: 10.1093/Nar/29.4.943  0.64
2001 Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA. A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Research. 29: 223-7. PMID 11125098 DOI: 10.1093/Nar/29.1.223  0.622
2001 Valdar WS, Thornton JM. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins. 42: 108-24. PMID 11093265 DOI: 10.1002/1097-0134(20010101)42:1<108::Aid-Prot110>3.0.Co;2-O  0.417
2000 Luscombe NM, Austin SE, Berman HM, Thornton JM. An overview of the structures of protein-DNA complexes. Genome Biology. 1: REVIEWS001. PMID 11104519 DOI: 10.1186/Gb-2000-1-1-Reviews001  0.41
2000 Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA. From structure to function: approaches and limitations. Nature Structural Biology. 7: 991-4. PMID 11104008 DOI: 10.1038/80784  0.433
2000 Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins. 41: 47-57. PMID 10944393 DOI: 10.1002/1097-0134(20001001)41:1<47::Aid-Prot80>3.0.Co;2-8  0.61
2000 Pearl F, Todd AE, Bray JE, Martin AC, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA. Using the CATH domain database to assign structures and functions to the genome sequences. Biochemical Society Transactions. 28: 269-75. PMID 10816141 DOI: 10.1042/Bst0280269  0.428
2000 Bray JE, Todd AE, Pearl FM, Thornton JM, Orengo CA. The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. Protein Engineering. 13: 153-65. PMID 10775657 DOI: 10.1093/Protein/13.3.153  0.484
2000 Taroni C, Jones S, Thornton JM. Analysis and prediction of carbohydrate binding sites. Protein Engineering. 13: 89-98. PMID 10708647 DOI: 10.1093/Protein/13.2.89  0.631
2000 Jones S, Marin A, Thornton JM. Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Engineering. 13: 77-82. PMID 10708645 DOI: 10.1093/Protein/13.2.77  0.633
2000 Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA. Assigning genomic sequences to CATH. Nucleic Acids Research. 28: 277-82. PMID 10592246 DOI: 10.1093/Nar/28.1.277  0.437
2000 Thornton J. THE EVOLUTION OF ENZYME STRUCTURE AND FUNCTION Biochemical Society Transactions. 28: A53-A53. DOI: 10.1042/Bst028A053  0.386
2000 Orengo CA, Pearl F, Bray J, Todd A, Thornton JM. Functional Insights from Structural Families Biochemical Society Transactions. 28: 22. DOI: 10.1042/Bst028A022C  0.313
1999 Nagano N, Hutchinson EG, Thornton JM. Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels. Protein Science : a Publication of the Protein Society. 8: 2072-84. PMID 10548053 DOI: 10.1110/Ps.8.10.2072  0.377
1999 Thornton JM, Orengo CA, Todd AE, Pearl FM. Protein folds, functions and evolution. Journal of Molecular Biology. 293: 333-42. PMID 10529349 DOI: 10.1006/Jmbi.1999.3054  0.454
1999 Todd AE, Orengo CA, Thornton JM. Evolution of protein function, from a structural perspective. Current Opinion in Chemical Biology. 3: 548-56. PMID 10508675 DOI: 10.1016/S1367-5931(99)00007-1  0.45
1999 Orengo CA, Todd AE, Thornton JM. From protein structure to function. Current Opinion in Structural Biology. 9: 374-82. PMID 10361094 DOI: 10.1016/S0959-440X(99)80051-7  0.421
1999 Todd AE, Orengo CA, Thornton JM. DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts. Protein Engineering. 12: 375-9. PMID 10360977 DOI: 10.1093/Protein/12.5.375  0.398
1999 Gilbert D, Westhead D, Nagano N, Thornton J. Motif-based searching in TOPS protein topology databases. Bioinformatics (Oxford, England). 15: 317-26. PMID 10320400 DOI: 10.1093/Bioinformatics/15.4.317  0.436
1999 Harding SE, Horton JC, Jones S, Thornton JM, Winzor DJ. COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules. Biophysical Journal. 76: 2432-8. PMID 10233060 DOI: 10.1016/S0006-3495(99)77398-4  0.563
1999 Salem GM, Hutchinson EG, Orengo CA, Thornton JM. Correlation of observed fold frequency with the occurrence of local structural motifs. Journal of Molecular Biology. 287: 969-81. PMID 10222204 DOI: 10.1006/Jmbi.1999.2642  0.336
1999 Jones S, van Heyningen P, Berman HM, Thornton JM. Protein-DNA interactions: A structural analysis. Journal of Molecular Biology. 287: 877-96. PMID 10222198 DOI: 10.1006/Jmbi.1999.2659  0.635
1999 MacArthur MW, Thornton JM. Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states? Acta Crystallographica. Section D, Biological Crystallography. 55: 994-1004. PMID 10216296 DOI: 10.1107/S0907444999002231  0.672
1999 Westhead DR, Slidel TW, Flores TP, Thornton JM. Protein structural topology: Automated analysis and diagrammatic representation. Protein Science : a Publication of the Protein Society. 8: 897-904. PMID 10211836 DOI: 10.1110/Ps.8.4.897  0.429
1999 de la Cruz X, Thornton JM. Factors limiting the performance of prediction-based fold recognition methods. Protein Science : a Publication of the Protein Society. 8: 750-9. PMID 10211821 DOI: 10.1110/Ps.8.4.750  0.334
1999 Gardner S, Thornton J. Iditis: protein structure database. Acta Crystallographica. Section D, Biological Crystallography. 54: 1071-7. PMID 10089482 DOI: 10.1107/S0907444998007112  0.443
1999 Kasuya A, Thornton JM. Three-dimensional structure analysis of PROSITE patterns. Journal of Molecular Biology. 286: 1673-91. PMID 10064723 DOI: 10.1006/Jmbi.1999.2581  0.336
1999 Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM. The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Research. 27: 275-9. PMID 9847200 DOI: 10.1093/Nar/27.1.275  0.471
1999 Mitchell JBO, Laskowski RA, Alex A, Forster MJ, Thornton JM. BLEEP?potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data Journal of Computational Chemistry. 20: 1177-1185. DOI: 10.1002/(Sici)1096-987X(199908)20:11<1177::Aid-Jcc8>3.0.Co;2-0  0.651
1999 Mitchell JBO, Laskowski RA, Alex A, Thornton JM. BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential Journal of Computational Chemistry. 20: 1165-1176. DOI: 10.1002/(Sici)1096-987X(199908)20:11<1165::Aid-Jcc7>3.0.Co;2-A  0.327
1998 Orengo CA, Martin AM, Hutchinson G, Jones S, Jones DT, Michie AD, Swindells MB, Thornton JM. Classifying a protein in the CATH database of domain structures. Acta Crystallographica. Section D, Biological Crystallography. 54: 1155-67. PMID 10089492 DOI: 10.1107/S0907444998007501  0.673
1998 Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou M, Thornton JM. New tools and resources for analysing protein structures and their interactions. Acta Crystallographica. Section D, Biological Crystallography. 54: 1132-8. PMID 10089489 DOI: 10.1107/S0907444998007318  0.801
1998 Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM. Contemporary approaches to protein structure classification. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 20: 884-91. PMID 9872054 DOI: 10.1002/(Sici)1521-1878(199811)20:11<884::Aid-Bies3>3.0.Co;2-H  0.458
1998 Milburn D, Laskowski RA, Thornton JM. Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Protein Engineering. 11: 855-9. PMID 9862203 DOI: 10.1093/Protein/11.10.855  0.706
1998 Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN. Determinants of strand register in antiparallel beta-sheets of proteins. Protein Science : a Publication of the Protein Society. 7: 2287-300. PMID 9827995 DOI: 10.1002/Pro.5560071106  0.313
1998 Laskowski RA, MacArthur MW, Thornton JM. Validation of protein models derived from experiment. Current Opinion in Structural Biology. 8: 631-9. PMID 9818269 DOI: 10.1016/S0959-440X(98)80156-5  0.782
1998 Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends in Biochemical Sciences. 23: 358-61. PMID 9787643 DOI: 10.1016/S0968-0004(98)01253-5  0.303
1998 Westhead DR, Thornton JM. Protein structure prediction. Current Opinion in Biotechnology. 9: 383-9. PMID 9751638 DOI: 10.1016/S0958-1669(98)80012-8  0.406
1998 Zuccotto F, Martin AC, Laskowski RA, Thornton JM, Gilbert IH. Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania. Journal of Computer-Aided Molecular Design. 12: 241-57. PMID 9749368 DOI: 10.1023/A:1016085005275  0.66
1998 Bloch C, Patel SU, Baud F, Zvelebil MJ, Carr MD, Sadler PJ, Thornton JM. 1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins. Proteins. 32: 334-49. PMID 9715910 DOI: 10.1002/(Sici)1097-0134(19980815)32:3<334::Aid-Prot9>3.0.Co;2-H  0.398
1998 Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM. Protein folds and functions. Structure (London, England : 1993). 6: 875-84. PMID 9687369 DOI: 10.1016/S0969-2126(98)00089-6  0.805
1998 Hubbard SJ, Beynon RJ, Thornton JM. Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures. Protein Engineering. 11: 349-59. PMID 9681867 DOI: 10.1093/Protein/11.5.349  0.385
1998 Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM. Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Science : a Publication of the Protein Society. 7: 233-42. PMID 9521098 DOI: 10.1002/Pro.5560070202  0.638
1998 Smith GP, Patel SU, Windass JD, Thornton JM, Winter G, Griffiths AD. Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. Journal of Molecular Biology. 277: 317-32. PMID 9514763 DOI: 10.1006/Jmbi.1997.1621  0.41
1998 Westhead DR, Hatton DC, Thornton JM. An atlas of protein topology cartoons available on the World-Wide Web. Trends in Biochemical Sciences. 23: 35-6. PMID 9478134 DOI: 10.1016/S0968-0004(97)01161-4  0.359
1998 Patel SU, Osborn R, Rees S, Thornton JM. Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1). Biochemistry. 37: 983-90. PMID 9454588 DOI: 10.1021/Bi971747D  0.349
1997 Martin AC, MacArthur MW, Thornton JM. Assessment of comparative modeling in CASP2. Proteins. 14-28. PMID 9485491 DOI: 10.1002/(Sici)1097-0134(1997)1+<14::Aid-Prot4>3.0.Co;2-O  0.675
1997 Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM. PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends in Biochemical Sciences. 22: 488-90. PMID 9433130 DOI: 10.1016/S0968-0004(97)01140-7  0.675
1997 Williams MA, Thornton JM, Goodfellow JM. Modelling protein unfolding: hen egg-white lysozyme. Protein Engineering. 10: 895-903. PMID 9415439 DOI: 10.1093/Protein/10.8.895  0.408
1997 Luscombe NM, Laskowski RA, Thornton JM. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Research. 25: 4940-5. PMID 9396800 DOI: 10.1093/Nar/25.24.4940  0.69
1997 Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Science : a Publication of the Protein Society. 6: 2308-23. PMID 9385633 DOI: 10.1002/Pro.5560061104  0.431
1997 Mitchell JB, Laskowski RA, Thornton JM. Non-randomness in side-chain packing: the distribution of interplanar angles. Proteins. 29: 370-80. PMID 9365991 DOI: 10.1002/(Sici)1097-0134(199711)29:3<370::Aid-Prot10>3.0.Co;2-K  0.633
1997 Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure (London, England : 1993). 5: 1093-108. PMID 9309224 DOI: 10.1016/S0969-2126(97)00260-8  0.687
1997 Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. Journal of Molecular Biology. 272: 133-43. PMID 9299343 DOI: 10.1006/Jmbi.1997.1233  0.666
1997 Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. Journal of Molecular Biology. 272: 121-32. PMID 9299342 DOI: 10.1006/Jmbi.1997.1234  0.63
1997 Doig AJ, MacArthur MW, Stapley BJ, Thornton JM. Structures of N-termini of helices in proteins. Protein Science : a Publication of the Protein Society. 6: 147-55. PMID 9007987 DOI: 10.1002/Pro.5560060117  0.638
1996 Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular Nmr. 8: 477-86. PMID 9008363 DOI: 10.1007/Bf00228148  0.792
1996 MacArthur MW, Thornton JM. Deviations from planarity of the peptide bond in peptides and proteins. Journal of Molecular Biology. 264: 1180-95. PMID 9000639 DOI: 10.1006/Jmbi.1996.0705  0.673
1996 Laskowski RA, Luscombe NM, Swindells MB, Thornton JM. Protein clefts in molecular recognition and function. Protein Science : a Publication of the Protein Society. 5: 2438-52. PMID 8976552 DOI: 10.1002/Pro.5560051206  0.707
1996 Viles JH, Mitchell JB, Gough SL, Doyle PM, Harris CJ, Sadler PJ, Thornton JM. 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. European Journal of Biochemistry / Febs. 242: 352-62. PMID 8973654 DOI: 10.1111/J.1432-1033.1996.0352R.X  0.352
1996 Martin AC, Thornton JM. Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. Journal of Molecular Biology. 263: 800-15. PMID 8947577 DOI: 10.1006/Jmbi.1996.0617  0.387
1996 Moodie SL, Mitchell JB, Thornton JM. Protein recognition of adenylate: an example of a fuzzy recognition template. Journal of Molecular Biology. 263: 486-500. PMID 8918603 DOI: 10.1006/Jmbi.1996.0591  0.344
1996 MacCallum RM, Martin AC, Thornton JM. Antibody-antigen interactions: contact analysis and binding site topography. Journal of Molecular Biology. 262: 732-45. PMID 8876650 DOI: 10.1006/Jmbi.1996.0548  0.316
1996 Jones DT, Moody CM, Uppenbrink J, Viles JH, Doyle PM, Harris CJ, Pearl LH, Sadler PJ, Thornton JM. 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. Proteins. 24: 502-13. PMID 8859998 DOI: 10.1002/(Sici)1097-0134(199604)24:4<502::Aid-Prot9>3.0.Co;2-F  0.387
1996 Doyle PM, Harris JC, Moody CM, Sadler PJ, Sims M, Thornton JM, Uppenbrink J, Viles JH. Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic. International Journal of Peptide and Protein Research. 47: 427-36. PMID 8836770 DOI: 10.1111/J.1399-3011.1996.Tb01093.X  0.305
1996 Michie AD, Orengo CA, Thornton JM. Analysis of domain structural class using an automated class assignment protocol. Journal of Molecular Biology. 262: 168-85. PMID 8831787 DOI: 10.1006/Jmbi.1996.0506  0.403
1996 Martin AC, Toda K, Stirk HJ, Thornton JM. Long loops in proteins. Protein Engineering. 8: 1093-101. PMID 8819975 DOI: 10.1093/Protein/8.11.1093  0.355
1996 Wallace AC, Laskowski RA, Thornton JM. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Science : a Publication of the Protein Society. 5: 1001-13. PMID 8762132 DOI: 10.1002/Pro.5560050603  0.73
1996 Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J. Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium. Trends in Biochemical Sciences. 21: 251-6. PMID 8755246 DOI: 10.1016/0968-0004(96)10037-2  0.335
1996 Hutchinson EG, Thornton JM. PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Science : a Publication of the Protein Society. 5: 212-20. PMID 8745398 DOI: 10.1002/Pro.5560050204  0.324
1996 Jones DT, Thornton JM. Potential energy functions for threading. Current Opinion in Structural Biology. 6: 210-6. PMID 8728653 DOI: 10.1016/S0959-440X(96)80076-5  0.357
1996 Jones DT, Miller RT, Thornton JM. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins. 23: 387-97. PMID 8710831 DOI: 10.1002/Prot.340230312  0.364
1996 Wallace AC, Laskowski RA, Singh J, Thornton JM. Molecular recognition by proteins: protein-ligand interactions from a structural perspective. Biochemical Society Transactions. 24: 280-4. PMID 8674687 DOI: 10.1042/Bst0240280  0.699
1996 Laskowski RA, Thornton JM, Humblet C, Singh J. X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. Journal of Molecular Biology. 259: 175-201. PMID 8648645 DOI: 10.1006/Jmbi.1996.0311  0.685
1996 Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. Journal of Molecular Biology. 255: 494-506. PMID 8568893 DOI: 10.1006/Jmbi.1996.0041  0.701
1996 Miller RT, Jones DT, Thornton JM. Protein fold recognition by sequence threading: tools and assessment techniques. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 10: 171-8. PMID 8566539 DOI: 10.1096/Fasebj.10.1.8566539  0.402
1996 Jones S, Thornton JM. Principles of protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 93: 13-20. PMID 8552589 DOI: 10.1073/Pnas.93.1.13  0.645
1996 Orengo CA, Swindells MB, Michie AD, Zvelebil MJ, Driscoll PC, Waterfield MD, Thornton JM. Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity. Protein Science : a Publication of the Protein Society. 4: 1977-83. PMID 8535234 DOI: 10.1002/Pro.5560041003  0.376
1996 Thornton JM, Hutchinson EG, Jones S, Laskowski RA, MacArthur MW, Michie A, Orengo CM. Protein structures: their validation fold classification and interactions Acta Crystallographica Section a Foundations of Crystallography. 52: C6-C6. DOI: 10.1107/S0108767396098789  0.802
1996 Goodfellow JM, Knaggs M, Williams MA, Thornton JM. Modelling protein unfolding: a solvent insertion protocol Faraday Discussions. 103: 339. DOI: 10.1039/Fd9960300339  0.407
1995 Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature. 372: 631-4. PMID 7990952 DOI: 10.1038/372631A0  0.461
1995 Williams MA, Goodfellow JM, Thornton JM. Buried waters and internal cavities in monomeric proteins. Protein Science : a Publication of the Protein Society. 3: 1224-35. PMID 7987217 DOI: 10.1002/Pro.5560030808  0.337
1995 Thornton JM, Jones DT, MacArthur MW, Orengo CM, Swindells MB. Protein folds: towards understanding folding from inspection of native structures. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 348: 71-9. PMID 7770489 DOI: 10.1098/Rstb.1995.0047  0.733
1995 Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Progress in Biophysics and Molecular Biology. 63: 31-65. PMID 7746868 DOI: 10.1016/0079-6107(94)00008-W  0.658
1995 Swindells MB, MacArthur MW, Thornton JM. Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nature Structural Biology. 2: 596-603. PMID 7664128 DOI: 10.1038/Nsb0795-596  0.69
1995 Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Engineering. 8: 127-34. PMID 7630882 DOI: 10.1093/Protein/8.2.127  0.671
1995 Mitchell JBO, Thornton JM, Price SL. Modelling the interactions of protein side-chains Molecular Engineering. 5: 89-105. DOI: 10.1007/978-94-011-0497-5_11  0.544
1994 Swindells MB, Thornton JM. A study of structural determinants in the interleukin-1 fold. Protein Engineering. 6: 711-5. PMID 8248094 DOI: 10.1093/Protein/6.7.711  0.404
1994 Mitchell JB, Nandi CL, McDonald IK, Thornton JM, Price SL. Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding? Journal of Molecular Biology. 239: 315-31. PMID 8196060 DOI: 10.1006/Jmbi.1994.1370  0.501
1994 Flores TP, Moss DS, Thornton JM. An algorithm for automatically generating protein topology cartoons. Protein Engineering. 7: 31-7. PMID 8140092 DOI: 10.1093/Protein/7.1.31  0.31
1994 Jones DT, Taylor WR, Thornton JM. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33: 3038-49. PMID 8130217 DOI: 10.1021/Bi00176A037  0.34
1994 Jones DT, Taylor WR, Thornton JM. A mutation data matrix for transmembrane proteins. Febs Letters. 339: 269-75. PMID 8112466 DOI: 10.1016/0014-5793(94)80429-X  0.339
1994 Orengo CA, Thornton JM. Alpha plus beta folds revisited: some favoured motifs. Structure (London, England : 1993). 1: 105-20. PMID 8069624 DOI: 10.1016/0969-2126(93)90026-D  0.337
1994 MacArthur MW, Driscoll PC, Thornton JM. NMR and crystallography--complementary approaches to structure determination. Trends in Biotechnology. 12: 149-53. PMID 7764895 DOI: 10.1016/0167-7799(94)90074-4  0.714
1994 Hubbard SJ, Eisenmenger F, Thornton JM. Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Protein Science : a Publication of the Protein Society. 3: 757-68. PMID 7520312 DOI: 10.1002/Pro.5560030505  0.384
1994 Stirk HJ, Thornton JM. The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions. Protein Engineering. 7: 47-56. PMID 7511245 DOI: 10.1093/Protein/7.1.47  0.334
1994 MacArthur MW, Laskowski RA, Thornton JM. Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy Current Opinion in Structural Biology. 4: 731-737. DOI: 10.1016/S0959-440X(94)90172-4  0.793
1993 Orengo CA, Flores TP, Jones DT, Taylor WR, Thornton JM. Recurring structural motifs in proteins with different functions. Current Biology : Cb. 3: 131-9. PMID 15335780 DOI: 10.1016/0960-9822(93)90254-L  0.466
1993 Laskowski RA, Moss DS, Thornton JM. Main-chain bond lengths and bond angles in protein structures. Journal of Molecular Biology. 231: 1049-67. PMID 8515464 DOI: 10.1006/Jmbi.1993.1351  0.659
1993 Hutchinson EG, Thornton JM. The Greek key motif: extraction, classification and analysis. Protein Engineering. 6: 233-45. PMID 8506258 DOI: 10.1093/Protein/6.3.233  0.388
1993 Moodie SL, Thornton JM. A study into the effects of protein binding on nucleotide conformation. Nucleic Acids Research. 21: 1369-80. PMID 8464727 DOI: 10.1093/Nar/21.6.1369  0.432
1993 Sibanda BL, Thornton JM. Accommodating sequence changes in beta-hairpins in proteins. Journal of Molecular Biology. 229: 428-47. PMID 8429555 DOI: 10.1006/Jmbi.1993.1044  0.349
1993 Orengo CA, Flores TP, Taylor WR, Thornton JM. Identification and classification of protein fold families. Protein Engineering. 6: 485-500. PMID 8415576 DOI: 10.1093/Protein/6.5.485  0.405
1993 MacArthur MW, Thornton JM. Conformational analysis of protein structures derived from NMR data. Proteins. 17: 232-51. PMID 8272423 DOI: 10.1002/Prot.340170303  0.706
1993 Flores TP, Orengo CA, Moss DS, Thornton JM. Comparison of conformational characteristics in structurally similar protein pairs. Protein Science : a Publication of the Protein Society. 2: 1811-26. PMID 8268794 DOI: 10.1002/Pro.5560021104  0.438
1993 Jones D, Thornton J. Protein fold recognition. Journal of Computer-Aided Molecular Design. 7: 439-56. PMID 8229094 DOI: 10.1007/Bf02337560  0.44
1993 Zvelebil MJJM, Tang L, Cookson E, Selkirk ME, Thornton JM. Molecular modelling and epitope prediction of gp29 from lymphatic filariae. Molecular and Biochemical Parasitology. 58: 145-153. PMID 7681545 DOI: 10.1016/0166-6851(93)90098-I  0.367
1993 Hubbard SJ, Thornton JM, Campbell SF. Substrate recognition by proteinases. Faraday Discussions. 13-23. PMID 1290927 DOI: 10.1039/Fd9929300013  0.408
1993 Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures Journal of Applied Crystallography. 26: 283-291. DOI: 10.1107/S0021889892009944  0.796
1993 Thornton JM, Macarthur MW, Mcdonald IK, Jones DT, Mitchell JBO, Nandi CL, Price SL, Zvelebil MJJM. Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them Philosophical Transactions of the Royal Society A. 345: 113-129. DOI: 10.1098/Rsta.1993.0123  0.602
1993 Jones DT, Orengo C, Taylor WR, Thornton J. Progress Towards Recognising Protein Folds from Amino Acid Sequence Protein Engineering Design & Selection. 6: 124-124. DOI: 10.1093/Protein/6.Supplement.124-B  0.336
1993 Mitchell JBO, Nandi CL, Thornton JM, Price SL, Singh J, Snarey M. A comparison of three theoretical approaches to the study of side-chain interactions in proteins Journal of the Chemical Society, Faraday Transactions. 89: 2619. DOI: 10.1039/Ft9938902619  0.52
1993 Mitchell JBO, Nandi CL, Ali S, McDonald IK, Thornton JM, Price SL, Singh J. Amino/aromatic interactions Nature. 366: 413-413. DOI: 10.1038/366413A0  0.483
1993 Swindells MB, Orengo CA, Jones DT, Pearl LH, Thornton JM. Shared structural motif in proteins Nature. 365: 21-21. DOI: 10.1038/365021B0  0.436
1992 Sibanda BL, Thornton JM. Conformation of beta hairpins in protein structures: classification and diversity in homologous structures. Methods in Enzymology. 202: 59-82. PMID 1784189 DOI: 10.1016/0076-6879(91)02007-V  0.431
1992 Stirk HJ, Woolfson DN, Hutchinson EG, Thornton JM. Depicting topology and handedness in jellyroll structures. Febs Letters. 308: 1-3. PMID 1644197 DOI: 10.1016/0014-5793(92)81036-L  0.321
1992 Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences : Cabios. 8: 275-82. PMID 1633570 DOI: 10.1093/Bioinformatics/8.3.275  0.307
1992 Mitchell JB, Thornton JM, Singh J, Price SL. Towards an understanding of the arginine-aspartate interaction. Journal of Molecular Biology. 226: 251-62. PMID 1619654 DOI: 10.1016/0022-2836(92)90137-9  0.518
1992 Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature. 358: 86-9. PMID 1614539 DOI: 10.1038/358086A0  0.446
1992 Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins. 12: 345-64. PMID 1579569 DOI: 10.1002/Prot.340120407  0.685
1992 Thornton JM. Lessons from analyzing protein structures Current Opinion in Structural Biology. 2: 888-894. DOI: 10.1016/0959-440X(92)90115-N  0.432
1991 Hutchinson EG, Thornton JM. HERA--a program to draw schematic diagrams of protein secondary structures. Proteins. 8: 203-12. PMID 2281084 DOI: 10.1002/Prot.340080303  0.349
1991 Hunter CA, Singh J, Thornton JM. π-π interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins Journal of Molecular Biology. 218: 837-846. PMID 2023252 DOI: 10.1016/0022-2836(91)90271-7  0.334
1991 MacArthur MW, Thornton JM. Influence of proline residues on protein conformation. Journal of Molecular Biology. 218: 397-412. PMID 2010917 DOI: 10.1016/0022-2836(91)90721-H  0.687
1991 Thornton JM, Flores TP, Jones DT, Swindells MB. Protein structure. Prediction of progress at last. Nature. 354: 105-6. PMID 1944583 DOI: 10.1038/354105A0  0.388
1991 Thanki N, Umrania Y, Thornton JM, Goodfellow JM. Analysis of protein main-chain solvation as a function of secondary structure. Journal of Molecular Biology. 221: 669-91. PMID 1920440 DOI: 10.1016/0022-2836(91)80080-E  0.343
1991 Singh J, Saldanha J, Thornton JM. A novel method for the modelling of peptide ligands to their receptors. Protein Engineering. 4: 251-61. PMID 1857711 DOI: 10.1093/Protein/4.3.251  0.372
1991 Swindells MB, Thornton JM. Structure prediction and modelling. Current Opinion in Biotechnology. 2: 512-9. PMID 1367669 DOI: 10.1016/0958-1669(91)90074-F  0.427
1991 Swindells MB, Thornton JM. Modelling by homology Current Opinion in Structural Biology. 1: 219-223. DOI: 10.1016/0959-440X(91)90064-Z  0.413
1991 Garratt RC, Thornton JM, Taylor WR. An extension of secondary structure prediction towards the production of tertiary structure Febs Letters. 280: 141-146. DOI: 10.1016/0014-5793(91)80223-P  0.586
1990 Wilmot CM, Thornton JM. Beta-turns and their distortions: a proposed new nomenclature. Protein Engineering. 3: 479-93. PMID 2371257 DOI: 10.1093/Protein/3.6.479  0.61
1990 Singh J, Thornton JM. SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups. Journal of Molecular Biology. 211: 595-615. PMID 2308168 DOI: 10.1016/0022-2836(90)90268-Q  0.32
1990 Thanki N, Thornton JM, Goodfellow JM. Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins. Protein Engineering. 3: 495-508. PMID 2115163 DOI: 10.1093/Protein/3.6.495  0.341
1989 Rooman MJ, Wodak SJ, Thornton JM. Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. Protein Engineering. 3: 23-7. PMID 2813339 DOI: 10.1093/Protein/3.1.23  0.384
1989 Reid LS, Thornton JM. Rebuilding flavodoxin from C alpha coordinates: a test study. Proteins. 5: 170-82. PMID 2748580 DOI: 10.1002/Prot.340050212  0.367
1989 Thornton JM, Gardner SP. Protein motifs and data-base searching. Trends in Biochemical Sciences. 14: 300-4. PMID 2672454 DOI: 10.1016/0968-0004(89)90069-8  0.45
1989 Sibanda BL, Blundell TL, Thornton JM. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. Journal of Molecular Biology. 206: 759-77. PMID 2500530 DOI: 10.1016/0022-2836(89)90583-4  0.478
1989 Goodfellow JM, Thanki N, Thornton JM. Preliminary Analysis of Water Molecule Distributions in Proteins Molecular Simulation. 3: 167-182. DOI: 10.1080/08927028908034626  0.362
1988 Singh J, Thornton JM, Snarey M, Campbell SF. The geometries of interacting arginine-carboxyls in proteins. Febs Letters. 224: 161-71. PMID 3678490 DOI: 10.1016/0014-5793(87)80441-6  0.304
1988 Barlow DJ, Thornton JM. Helix geometry in proteins. Journal of Molecular Biology. 201: 601-19. PMID 3418712 DOI: 10.1016/0022-2836(88)90641-9  0.331
1988 Thornton JM, Sibanda BL, Edwards MS, Barlow DJ. Analysis, design and modification of loop regions in proteins. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 8: 63-9. PMID 3282506 DOI: 10.1002/Bies.950080205  0.406
1988 Thornton JM, Singh J, Campbell S, Blundell TL. Protein-protein recognition via side-chain interactions. Biochemical Society Transactions. 16: 927-30. PMID 3224756 DOI: 10.1042/Bst0160927  0.511
1988 Wilmot CM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. Journal of Molecular Biology. 203: 221-32. PMID 3184187 DOI: 10.1016/0022-2836(88)90103-9  0.588
1988 Thanki N, Thornton JM, Goodfellow JM. Distributions of water around amino acid residues in proteins. Journal of Molecular Biology. 202: 637-57. PMID 3172231 DOI: 10.1016/0022-2836(88)90292-6  0.321
1987 Blundell TL, Sibanda BL, Sternberg MJ, Thornton JM. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 326: 347-52. PMID 3550471 DOI: 10.1038/326347A0  0.551
1987 Edwards MS, Sternberg MJE, Thornton JM. Structural and sequence patterns in the loops of βαβ units Protein Engineering, Design and Selection. 1: 173-181. PMID 3507703 DOI: 10.1093/Protein/1.3.173  0.337
1986 Barlow DJ, Thornton JM. The distribution of charged groups in proteins. Biopolymers. 25: 1717-33. PMID 3768483 DOI: 10.1002/Bip.360250913  0.317
1986 Barlow DJ, Edwards MS, Thornton JM. Continuous and discontinuous protein antigenic determinants Nature. 322: 747-748. PMID 2427953 DOI: 10.1038/322747A0  0.364
1986 Blundell TL, Barlow D, Sibanda BL, Thornton JM, Taylor W, Tickle IJ, Sternberg MJE, Pitts JE, Haneef I, Hemmings AM, Robson B. Three-dimensional structural aspects of the design of new protein molecules Philosophical Transactions of the Royal Society A. 317: 333-344. DOI: 10.1098/Rsta.1986.0043  0.433
1985 Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature. 316: 170-4. PMID 4010788 DOI: 10.1038/316170A0  0.352
1985 Garratt RC, Taylor WR, Thornton JM. The influence of tertiary structure on secondary structure prediction Febs Letters. 188: 59-62. DOI: 10.1016/0014-5793(85)80874-7  0.596
1984 Taylor WR, Thornton JM. Recognition of super-secondary structure in proteins Journal of Molecular Biology. 173: 487-514. PMID 6708107 DOI: 10.1016/0022-2836(84)90393-0  0.405
1984 Blundell T, Barlow D, Borkakoti N, Thornton J. Solvent-induced distortions and the curvature of alpha-helices. Nature. 306: 281-3. PMID 6646210 DOI: 10.1038/306281A0  0.466
1984 Pearl LH, Tickle IJ, Honegger A, Taylor GL, Barlow DJ, Thornton JM, Haneef I, Taylor WR, Blundell TL, Busetta B. The applications of computer calligraphics in protein engineering and drug design Acta Crystallographica Section a Foundations of Crystallography. 40: C42-C42. DOI: 10.1107/S0108767384098512  0.444
1983 Barlow DJ, Thornton JM. Ion-pairs in proteins. Journal of Molecular Biology. 168: 867-85. PMID 6887253 DOI: 10.1016/S0022-2836(83)80079-5  0.349
1983 Thornton JM, Sibanda BL. Amino and carboxy-terminal regions in globular proteins. Journal of Molecular Biology. 167: 443-60. PMID 6864804 DOI: 10.1016/S0022-2836(83)80344-1  0.404
1983 Taylor WR, Thornton JM. Prediction of super-secondary structure in proteins Nature. 301: 540-542. PMID 6823335 DOI: 10.1038/301540A0  0.398
1982 Thornton JM, Chakauya BL. Conformation of terminal regions in proteins. Nature. 298: 296-7. PMID 7088178 DOI: 10.1038/298296A0  0.342
1982 Thornton JM. Electrostatic interactions in proteins. Nature. 295: 13-4. PMID 7057870 DOI: 10.1038/295013A0  0.324
1981 Thornton JM. Disulphide bridges in globular proteins Journal of Molecular Biology. 151: 261-287. PMID 7338898 DOI: 10.1016/0022-2836(81)90515-5  0.385
1981 Thornton JM. Some principles of protein structure Acta Crystallographica Section a Foundations of Crystallography. 37: C18-C19. DOI: 10.1107/S0108767381099005  0.305
1979 Sternberg MJ, Thornton JM. Prediction of protein structure from amino acid sequence. Biochemical Society Transactions. 6: 1119-23. PMID 744369 DOI: 10.1042/Bst0061119  0.42
1978 Sternberg MJ, Thornton JM. On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets. Journal of Molecular Biology. 115: 1-17. PMID 926175 DOI: 10.1016/0022-2836(77)90242-X  0.327
1978 Phillips DC, Sternberg MJ, Thornton JM, Wilson IA. An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase. Journal of Molecular Biology. 119: 329-51. PMID 633372 DOI: 10.1016/0022-2836(78)90440-0  0.63
1978 Sternberg MJ, Thornton JM. Prediction of protein structure from amino acid sequence. Nature. 271: 15-20. PMID 342964 DOI: 10.1038/271015A0  0.43
1977 Phillips DC, Rivers PS, Sternberg MJ, Thornton JM, Wilson IA. An analysis of the three-dimensional structure of chicken triose phosphate isomerase. Biochemical Society Transactions. 5: 642-7. PMID 902882 DOI: 10.1042/Bst0050642  0.613
1977 Sternberg MJ, Thornton JM. On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets. Journal of Molecular Biology. 113: 401-18. PMID 886615 DOI: 10.1016/0022-2836(77)90149-8  0.357
1977 Sternberg MJ, Thornton JM. On the conformation of proteins: an analysis of beta-pleated sheets. Journal of Molecular Biology. 110: 285-96. PMID 845953 DOI: 10.1016/S0022-2836(77)80073-9  0.362
1977 Sternberg MJ, Thornton JM. On the conformation of proteins: the handedness of the connection between parallel beta-strands. Journal of Molecular Biology. 110: 269-83. PMID 845952 DOI: 10.1016/S0022-2836(77)80072-7  0.348
1977 Thornton JM, Bayley PM. Conformational energy calculations for dinucleotide molecules: a study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+). Biopolymers. 16: 1971-86. PMID 198038 DOI: 10.1002/Bip.1977.360160911  0.562
1976 Thornton JM, Bayley PM. Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate. Biopolymers. 15: 955-75. PMID 177120 DOI: 10.1002/Bip.1976.360150511  0.568
1975 Thornton JM, Bayley PM. Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate. The Biochemical Journal. 149: 585-96. PMID 1200996 DOI: 10.1042/Bj1490585  0.548
Show low-probability matches.