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Janet Thornton
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Research Profile (preview)
Concepts & Ideas
Chemicals & Drugs
Genes & Molecular Sequences
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Activities & Behaviors
Occupations
Physiology
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Network (preview)
36
Orengo, Christine
30
Laskowski, Roman
17
Todd, Annabel
14
Hutchinson, Gail
11
Pearl, Frances
10
Swindells, Mark
10
Nobeli, Irene
9
Bartlett, Gail
8
Bray, James
8
Rison, Stuart
7
Luscombe, Nicholas
6
Holliday, Gemma
6
Jones, Siân
6
Porter, Craig
6
Partridge, Linda
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All Publications
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2009: Selman Colin; Tullet Jennifer M A; Wieser Daniela; Irvine Elaine; Lingard Steven J; Choudhury Agharul I; Claret Marc; Al-Qassab Hind; Carmignac Danielle; Ramadani Faruk; Woods Angela; Robinson Iain C A; Schuster Eugene; Batterham Rachel L; Kozma Sara C; Thomas George; Carling David; Okkenhaug Klaus; Thornton Janet M; Partridge Linda; Gems David; Withers Dominic J
Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Science (New York, N.Y.) 2009;326(5949):140-4.
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2009: Macchiarulo Antonio; Thornton Janet M; Nobeli Irene
Mapping human metabolic pathways in the small molecule chemical space.
Journal of chemical information and modeling 2009;49(10):2272-89.
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2009: Furnham Nicholas; Garavelli John S; Apweiler Rolf; Thornton Janet M
Missing in action: enzyme functional annotations in biological databases.
Nature chemical biology 2009;5(8):521-5.
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2009: Laskowski Roman A; Thornton Janet M; Sternberg Michael J E
The fine details of evolution.
Biochemical Society transactions 2009;37(Pt 4):723-6.
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2009: Pellegrini-Calace Marialuisa; Maiwald Tim; Thornton Janet M
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
PLoS computational biology 2009;5(7):e1000440.
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2009: Holliday Gemma L; Mitchell John B O; Thornton Janet M
Understanding the functional roles of amino acid residues in enzyme catalysis.
Journal of molecular biology 2009;390(3):560-77.
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2009: Laskowski Roman A; Gerick Fabian; Thornton Janet M
The structural basis of allosteric regulation in proteins.
FEBS letters 2009;583(11):1692-8.
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2009: Andreini Claudia; Bertini Ivano; Cavallaro Gabriele; Najmanovich Rafael J; Thornton Janet M
Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Journal of molecular biology 2009;388(2):356-80.
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2009: Talavera David; Laskowski Roman A; Thornton Janet M
WSsas: a web service for the annotation of functional residues through structural homologues.
Bioinformatics (Oxford, England) 2009;25(9):1192-4.
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2009: Nobeli Irene; Favia Angelo D; Thornton Janet M
Protein promiscuity and its implications for biotechnology.
Nature biotechnology 2009;27(2):157-67.
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2008: Reeves Gabrielle A; Eilbeck Karen; Magrane Michele; O'Donovan Claire; Montecchi-Palazzi Luisa; Harris Midori A; Orchard Sandra; Jimenez Rafael C; Prlic Andreas; Hubbard Tim J P; Hermjakob Henning; Thornton Janet M
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Bioinformatics (Oxford, England) 2008;24(23):2767-72.
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2008: Torrance James W; Macarthur Malcolm W; Thornton Janet M
Evolution of binding sites for zinc and calcium ions playing structural roles.
Proteins 2008;71(2):813-30.
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2008: Selman Colin; Lingard Steven; Choudhury Agharul I; Batterham Rachel L; Claret Marc; Clements Melanie; Ramadani Faruk; Okkenhaug Klaus; Schuster Eugene; Blanc Eric; Piper Matthew D; Al-Qassab Hind; Speakman John R; Carmignac Danielle; Robinson Iain C A; Thornton Janet M; Gems David; Partridge Linda; Withers Dominic J
Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2008;22(3):807-18.
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2008: Laskowski Roman A; Thornton Janet M
Understanding the molecular machinery of genetics through 3D structures.
Nature reviews. Genetics 2008;9(2):141-51.
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2008: Favia Angelo D; Nobeli Irene; Glaser Fabian; Thornton Janet M
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Journal of molecular biology 2008;375(3):855-74.
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2008: Bashton Matthew; Nobeli Irene; Thornton Janet M
PROCOGNATE: a cognate ligand domain mapping for enzymes.
Nucleic acids research 2008;36(Database issue):D618-22.
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2008: Freilich Shiri; Goldovsky Leon; Ouzounis Christos A; Thornton Janet M
Metabolic innovations towards the human lineage.
BMC evolutionary biology 2008;8():247.
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2007: Ward Jonathan J; Thornton Janet M
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
PLoS computational biology 2007;3(10):1993-2002.
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2007: Holliday Gemma L; Thornton Janet M; Marquet Andrée; Smith Alison G; Rébeillé Fabrice; Mendel Ralf; Schubert Heidi L; Lawrence Andrew D; Warren Martin J
Evolution of enzymes and pathways for the biosynthesis of cofactors.
Natural product reports 2007;24(5):972-87.
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2007: Holliday Gemma L; Almonacid Daniel E; Mitchell John B O; Thornton Janet M
The chemistry of protein catalysis.
Journal of molecular biology 2007;372(5):1261-77.
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2007: Torrance James W; Holliday Gemma L; Mitchell John B O; Thornton Janet M
The geometry of interactions between catalytic residues and their substrates.
Journal of molecular biology 2007;369(4):1140-52.
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2007: Kahraman Abdullah; Morris Richard J; Laskowski Roman A; Thornton Janet M
Shape variation in protein binding pockets and their ligands.
Journal of molecular biology 2007;368(1):283-301.
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2007: Watson James D; Sanderson Steve; Ezersky Alexandra; Savchenko Alexei; Edwards Aled; Orengo Christine; Joachimiak Andrzej; Laskowski Roman A; Thornton Janet M
Towards fully automated structure-based function prediction in structural genomics: a case study.
Journal of molecular biology 2007;367(5):1511-22.
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2007: Najmanovich Rafael J; Allali-Hassani Abdellah; Morris Richard J; Dombrovsky Ludmila; Pan Patricia W; Vedadi Masoud; Plotnikov Alexander N; Edwards Aled; Arrowsmith Cheryl; Thornton Janet M
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Bioinformatics (Oxford, England) 2007;23(2):e104-9.
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2007: Greene Lesley H; Lewis Tony E; Addou Sarah; Cuff Alison; Dallman Tim; Dibley Mark; Redfern Oliver; Pearl Frances; Nambudiry Rekha; Reid Adam; Sillitoe Ian; Yeats Corin; Thornton Janet M; Orengo Christine A
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Nucleic acids research 2007;35(Database issue):D291-7.
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2007: Holliday Gemma L; Almonacid Daniel E; Bartlett Gail J; O'Boyle Noel M; Torrance James W; Murray-Rust Peter; Mitchell John B O; Thornton Janet M
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Nucleic acids research 2007;35(Database issue):D515-20.
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2007: McElwee Joshua J; Schuster Eugene; Blanc Eric; Piper Matthew D; Thomas James H; Patel Dhaval S; Selman Colin; Withers Dominic J; Thornton Janet M; Partridge Linda; Gems David
Evolutionary conservation of regulated longevity assurance mechanisms.
Genome biology 2007;8(7):R132.
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2007: Schuster Eugene F; Blanc Eric; Partridge Linda; Thornton Janet M
Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Genome biology 2007;8(6):R126.
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2007: Schuster Eugene F; Blanc Eric; Partridge Linda; Thornton Janet M
Correcting for sequence biases in present/absent calls.
Genome biology 2007;8(6):R125.
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2006: Bashton Matthew; Nobeli Irene; Thornton Janet M
Cognate ligand domain mapping for enzymes.
Journal of molecular biology 2006;364(4):836-52.
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2006: Selman Colin; Kerrison Nicola D; Cooray Anisha; Piper Matthew D W; Lingard Steven J; Barton Richard H; Schuster Eugene F; Blanc Eric; Gems David; Nicholson Jeremy K; Thornton Janet M; Partridge Linda; Withers Dominic J
Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.
Physiological genomics 2006;27(3):187-200.
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2006: Ranea Juan A G; Sillero Antonio; Thornton Janet M; Orengo Christine A
Protein superfamily evolution and the last universal common ancestor (LUCA).
Journal of molecular evolution 2006;63(4):513-25.
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2006: Whamond Gordon S; Thornton Janet M
An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Journal of molecular biology 2006;359(1):238-47.
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2006: Nobeli Irene; Thornton Janet M
A bioinformatician's view of the metabolome.
BioEssays : news and reviews in molecular, cellular and developmental biology 2006;28(5):534-45.
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2006: Reeves Gabrielle A; Thornton Janet M;
Integrating biological data through the genome.
Human molecular genetics 2006;15 Spec No 1():R81-7.
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2006: Jones David T; Sternberg Michael J E; Thornton Janet M
Introduction. Bioinformatics: from molecules to systems.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1467):389-91.
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2006: Stockwell Gareth R; Thornton Janet M
Conformational diversity of ligands bound to proteins.
Journal of molecular biology 2006;356(4):928-44.
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2006: Glaser Fabian; Morris Richard J; Najmanovich Rafael J; Laskowski Roman A; Thornton Janet M
A method for localizing ligand binding pockets in protein structures.
Proteins 2006;62(2):479-88.
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2006: Freilich Shiri; Massingham Tim; Blanc Eric; Goldovsky Leon; Thornton Janet M
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.
Genome biology 2006;7(10):R89.
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2005: Holliday Gemma L; Bartlett Gail J; Almonacid Daniel E; O'Boyle Noel M; Murray-Rust Peter; Thornton Janet M; Mitchell John B O
MACiE: a database of enzyme reaction mechanisms.
Bioinformatics (Oxford, England) 2005;21(23):4315-6.
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2005: Gutteridge Alex; Thornton Janet M
Understanding nature's catalytic toolkit.
Trends in biochemical sciences 2005;30(11):622-9.
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2005: Ponstingl Hannes; Kabir Thomas; Gorse Denise; Thornton Janet M
Morphological aspects of oligomeric protein structures.
Progress in biophysics and molecular biology 2005;89(1):9-35.
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2005: George Richard A; Spriggs Ruth V; Bartlett Gail J; Gutteridge Alex; MacArthur Malcolm W; Porter Craig T; Al-Lazikani Bissan; Thornton Janet M; Swindells Mark B
Effective function annotation through catalytic residue conservation.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(35):12299-304.
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2005: Laskowski Roman A; Watson James D; Thornton Janet M
Protein function prediction using local 3D templates.
Journal of molecular biology 2005;351(3):614-26.
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2005: Laskowski Roman A; Watson James D; Thornton Janet M
ProFunc: a server for predicting protein function from 3D structure.
Nucleic acids research 2005;33(Web Server issue):W89-93.
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2005: Najmanovich Rafael J; Torrance James W; Thornton Janet M
Prediction of protein function from structure: insights from methods for the detection of local structural similarities.
BioTechniques 2005;38(6):847, 849, 851.
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2005: Watson James D; Laskowski Roman A; Thornton Janet M
Predicting protein function from sequence and structural data.
Current opinion in structural biology 2005;15(3):275-84.
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2005: Freilich Shiri; Spriggs Ruth V; George Richard A; Al-Lazikani Bissan; Swindells Mark; Thornton Janet M
The complement of enzymatic sets in different species.
Journal of molecular biology 2005;349(4):745-63.
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2005: Todd Annabel E; Marsden Russell L; Thornton Janet M; Orengo Christine A
Progress of structural genomics initiatives: an analysis of solved target structures.
Journal of molecular biology 2005;348(5):1235-60.
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2005: Morris Richard J; Najmanovich Rafael J; Kahraman Abdullah; Thornton Janet M
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
Bioinformatics (Oxford, England) 2005;21(10):2347-55.
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2005: Torrance James W; Bartlett Gail J; Porter Craig T; Thornton Janet M
Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.
Journal of molecular biology 2005;347(3):565-81.
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2005: Nobeli Irene; Spriggs Ruth V; George Richard A; Thornton Janet M
A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.
Journal of molecular biology 2005;347(2):415-36.
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2005: Ranea Juan A G; Grant Alastair; Thornton Janet M; Orengo Christine A
Microeconomic principles explain an optimal genome size in bacteria.
Trends in genetics : TIG 2005;21(1):21-5.
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2005: Laskowski Roman A; Chistyakov Victor V; Thornton Janet M
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Nucleic acids research 2005;33(Database issue):D266-8.
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2005: Freilich Shiri; Massingham Tim; Bhattacharyya Sumit; Ponsting Hannes; Lyons Paul A; Freeman Tom C; Thornton Janet M
Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
Genome biology 2005;6(7):R56.
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2005: Orengo Christine A; Thornton Janet M
Protein families and their evolution-a structural perspective.
Annual review of biochemistry 2005;74():867-900.
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2005: Pellegrini-Calace Marialuisa; Thornton Janet M
Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.
Nucleic acids research 2005;33(7):2129-40.
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2004: Murray Kevin B; Taylor William R; Thornton Janet M
Toward the detection and validation of repeats in protein structure.
Proteins 2004;57(2):365-80.
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2004: Bray James E; Marsden Russell L; Rison Stuart C G; Savchenko Alexei; Edwards Aled M; Thornton Janet M; Orengo Christine A
A practical and robust sequence search strategy for structural genomics target selection.
Bioinformatics (Oxford, England) 2004;20(14):2288-95.
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2004: Shanahan H P; Thornton J M
An examination of the conservation of surface patch polarity for proteins.
Bioinformatics (Oxford, England) 2004;20(14):2197-204.
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2004: Macchiarulo Antonio; Nobeli Irene; Thornton Janet M
Ligand selectivity and competition between enzymes in silico.
Nature biotechnology 2004;22(8):1039-45.
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2004: George Richard A; Spriggs Ruth V; Thornton Janet M; Al-Lazikani Bissan; Swindells Mark B
SCOPEC: a database of protein catalytic domains.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i130-6.
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2004: Ranea Juan A G; Buchan Daniel W A; Thornton Janet M; Orengo Christine A
Evolution of protein superfamilies and bacterial genome size.
Journal of molecular biology 2004;336(4):871-87.
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2004: Jones Susan; Thornton Janet M
Searching for functional sites in protein structures.
Current opinion in chemical biology 2004;8(1):3-7.
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2004: Porter Craig T; Bartlett Gail J; Thornton Janet M
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
Nucleic acids research 2004;32(Database issue):D129-33.
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2004: Shanahan Hugh P; Garcia Mario A; Jones Susan; Thornton Janet M
Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
Nucleic acids research 2004;32(16):4732-41.
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2003: Jones Susan; Shanahan Hugh P; Berman Helen M; Thornton Janet M
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
Nucleic acids research 2003;31(24):7189-98.
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2003: Nobeli Irene; Ponstingl Hannes; Krissinel Eugene B; Thornton Janet M
A structure-based anatomy of the E.coli metabolome.
Journal of molecular biology 2003;334(4):697-719.
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2003: Barker Jonathan A; Thornton Janet M
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Bioinformatics (Oxford, England) 2003;19(13):1644-9.
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2003: Steward Robert E; MacArthur Malcolm W; Laskowski Roman A; Thornton Janet M
Molecular basis of inherited diseases: a structural perspective.
Trends in genetics : TIG 2003;19(9):505-13.
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2003: Bartlett Gail J; Borkakoti Neera; Thornton Janet M
Catalysing new reactions during evolution: economy of residues and mechanism.
Journal of molecular biology 2003;331(4):829-60.
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2003: Dawe Jennifer H; Porter Craig T; Thornton Janet M; Tabor Alethea B
A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
Proteins 2003;52(3):427-35.
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2003: Simeonidis Evangelos; Rison Stuart C G; Thornton Janet M; Bogle I David L; Papageorgiou Lazaros G
Analysis of metabolic networks using a pathway distance metric through linear programming.
Metabolic engineering 2003;5(3):211-9.
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2003: Nooren Irene M A; Thornton Janet M
Diversity of protein-protein interactions.
The EMBO journal 2003;22(14):3486-92.
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2003: Gutteridge Alex; Bartlett Gail J; Thornton Janet M
Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Journal of molecular biology 2003;330(4):719-34.
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2003: Jones Susan; Barker Jonathan A; Nobeli Irene; Thornton Janet M
Using structural motif templates to identify proteins with DNA binding function.
Nucleic acids research 2003;31(11):2811-23.
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2003: Watson James D; Todd Annabel E; Bray James; Laskowski Roman A; Edwards Aled; Joachimiak Andrzej; Orengo Christine A; Thornton Janet M
Target selection and determination of function in structural genomics.
IUBMB life 2003;55(4-5):249-55.
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2003: Shepherd Adrian J; Gorse Denise; Thornton Janet M
A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks.
Proteins 2003;50(2):290-302.
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2003: Nooren Irene M A; Thornton Janet M
Structural characterisation and functional significance of transient protein-protein interactions.
Journal of molecular biology 2003;325(5):991-1018.
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2003: Buchan Daniel W A; Rison Stuart C G; Bray James E; Lee David; Pearl Frances; Thornton Janet M; Orengo Christine A
Gene3D: structural assignments for the biologist and bioinformaticist alike.
Nucleic acids research 2003;31(1):469-73.
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2003: Jones Susan; Thornton Janet M
Protein-DNA Interactions: The Story so Far and a New Method for Prediction.
Comparative and functional genomics 2003;4(4):428-31.
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2003: Laskowski Roman A; Watson James D; Thornton Janet M
From protein structure to biochemical function?
Journal of structural and functional genomics 2003;4(2-3):167-77.
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2003: Bartlett Gail J; Todd Annabel E; Thornton Janet M
Inferring protein function from structure.
Methods of biochemical analysis 2003;44():387-407.
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2003: Orengo C A; Pearl F M G; Thornton J M
The CATH domain structure database.
Methods of biochemical analysis 2003;44():249-71.
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2002: Bartlett Gail J; Porter Craig T; Borkakoti Neera; Thornton Janet M
Analysis of catalytic residues in enzyme active sites.
Journal of molecular biology 2002;324(1):105-21.
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2002: Todd Annabel E; Orengo Christine A; Thornton Janet M
Sequence and structural differences between enzyme and nonenzyme homologs.
Structure (London, England : 1993) 2002;10(10):1435-51.
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2002: Nagano Nozomi; Orengo Christine A; Thornton Janet M
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
Journal of molecular biology 2002;321(5):741-65.
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2002: Todd Annabel E; Orengo Christine A; Thornton Janet M
Plasticity of enzyme active sites.
Trends in biochemical sciences 2002;27(8):419-26.
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2002: Steward Robert E; Thornton Janet M
Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
Proteins 2002;48(2):178-91.
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2002: Luscombe Nicholas M; Thornton Janet M
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Journal of molecular biology 2002;320(5):991-1009.
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2002: Rison Stuart C G; Thornton Janet M
Pathway evolution, structurally speaking.
Current opinion in structural biology 2002;12(3):374-82.
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2002: Rison Stuart C G; Teichmann Sarah A; Thornton Janet M
Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.
Journal of molecular biology 2002;318(3):911-32.
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2002: Buchan Daniel W A; Shepherd Adrian J; Lee David; Pearl Frances M G; Rison Stuart C G; Thornton Janet M; Orengo Christine A
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
Genome research 2002;12(3):503-14.
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2002: Murray Kevin B; Gorse Denise; Thornton Janet M
Wavelet transforms for the characterization and detection of repeating motifs.
Journal of molecular biology 2002;316(2):341-63.
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2002: Orengo Christine A; Bray James E; Buchan Daniel W A; Harrison Andrew; Lee David; Pearl Frances M G; Sillitoe Ian; Todd Annabel E; Thornton Janet M
The CATH protein family database: a resource for structural and functional annotation of genomes.
Proteomics 2002;2(1):11-21.
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2001: Teichmann S A; Rison S C; Thornton J M; Riley M; Gough J; Chothia C
Small-molecule metabolism: an enzyme mosaic.
Trends in biotechnology 2001;19(12):482-6.
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2001: Nagano N; Porter C T; Thornton J M
The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
Protein engineering 2001;14(11):845-55.
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2001: Nobeli I; Laskowski R A; Valdar W S; Thornton J M
On the molecular discrimination between adenine and guanine by proteins.
Nucleic acids research 2001;29(21):4294-309.
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2001: Valdar W S; Thornton J M
Conservation helps to identify biologically relevant crystal contacts.
Journal of molecular biology 2001;313(2):399-416.
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2001: Teichmann S A; Rison S C; Thornton J M; Riley M; Gough J; Chothia C
The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.
Journal of molecular biology 2001;311(4):693-708.
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2001: Luscombe N M; Laskowski R A; Thornton J M
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
Nucleic acids research 2001;29(13):2860-74.
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2001: Todd A E; Orengo C A; Thornton J M
Evolution of function in protein superfamilies, from a structural perspective.
Journal of molecular biology 2001;307(4):1113-43.
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2001: Jones S; Daley D T; Luscombe N M; Berman H M; Thornton J M
Protein-RNA interactions: a structural analysis.
Nucleic acids research 2001;29(4):943-54.
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2001: Thornton J M
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 2001;10(1):3-11.
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2001: Pearl F M; Martin N; Bray J E; Buchan D W; Harrison A P; Lee D; Reeves G A; Shepherd A J; Sillitoe I; Todd A E; Thornton J M; Orengo C A
A rapid classification protocol for the CATH Domain Database to support structural genomics.
Nucleic acids research 2001;29(1):223-7.
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2001: Valdar W S; Thornton J M
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
Proteins 2001;42(1):108-24.
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2000: Thornton J M; Todd A E; Milburn D; Borkakoti N; Orengo C A
From structure to function: approaches and limitations.
Nature structural biology 2000;7 Suppl():991-4.
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2000: Ponstingl H; Henrick K; Thornton J M
Discriminating between homodimeric and monomeric proteins in the crystalline state.
Proteins 2000;41(1):47-57.
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2000: Bray J E; Todd A E; Pearl F M; Thornton J M; Orengo C A
The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.
Protein engineering 2000;13(3):153-65.
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2000: Pearl F; Todd A E; Bray J E; Martin A C; Salamov A A; Suwa M; Swindells M B; Thornton J M; Orengo C A
Using the CATH domain database to assign structures and functions to the genome sequences.
Biochemical Society transactions 2000;28(2):269-75.
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2000: Jones S; Marin A; Thornton J M
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.
Protein engineering 2000;13(2):77-82.
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2000: Pearl F M; Lee D; Bray J E; Sillitoe I; Todd A E; Harrison A P; Thornton J M; Orengo C A
Assigning genomic sequences to CATH.
Nucleic acids research 2000;28(1):277-82.
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2000: Luscombe N M; Austin S E; Berman H M; Thornton J M
An overview of the structures of protein-DNA complexes.
Genome biology 2000;1(1):REVIEWS001.
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1999: Nagano N; Hutchinson E G; Thornton J M
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
Protein science : a publication of the Protein Society 1999;8(10):2072-84.
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1999: Thornton J M; Orengo C A; Todd A E; Pearl F M
Protein folds, functions and evolution.
Journal of molecular biology 1999;293(2):333-42.
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1999: Todd A E; Orengo C A; Thornton J M
Evolution of protein function, from a structural perspective.
Current opinion in chemical biology 1999;3(5):548-56.
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1999: Orengo C A; Todd A E; Thornton J M
From protein structure to function.
Current opinion in structural biology 1999;9(3):374-82.
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1999: Todd A E; Orengo C A; Thornton J M
DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.
Protein engineering 1999;12(5):375-9.
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1999: Shepherd A J; Gorse D; Thornton J M
Prediction of the location and type of beta-turns in proteins using neural networks.
Protein science : a publication of the Protein Society 1999;8(5):1045-55.
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1999: MacArthur M W; Thornton J M
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 1999;55(Pt 5):994-1004.
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1999: Salem G M; Hutchinson E G; Orengo C A; Thornton J M
Correlation of observed fold frequency with the occurrence of local structural motifs.
Journal of molecular biology 1999;287(5):969-81.
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1999: Jones S; van Heyningen P; Berman H M; Thornton J M
Protein-DNA interactions: A structural analysis.
Journal of molecular biology 1999;287(5):877-96.
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1999: Westhead D R; Slidel T W; Flores T P; Thornton J M
Protein structural topology: Automated analysis and diagrammatic representation.
Protein science : a publication of the Protein Society 1999;8(4):897-904.
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1999: de la Cruz X; Thornton J M
Factors limiting the performance of prediction-based fold recognition methods.
Protein science : a publication of the Protein Society 1999;8(4):750-9.
-
1999: Kasuya A; Thornton J M
Three-dimensional structure analysis of PROSITE patterns.
Journal of molecular biology 1999;286(5):1673-91.
-
1999: Orengo C A; Pearl F M; Bray J E; Todd A E; Martin A C; Lo Conte L; Thornton J M
The CATH Database provides insights into protein structure/function relationships.
Nucleic acids research 1999;27(1):275-9.
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1998: Orengo C A; Martin A M; Hutchinson G; Jones S; Jones D T; Michie A D; Swindells M B; Thornton J M
Classifying a protein in the CATH database of domain structures.
Acta crystallographica. Section D, Biological crystallography 1998;54(Pt 6 Pt 1):1155-67.
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1998: Luscombe N M; Laskowski R A; Westhead D R; Milburn D; Jones S; Karmirantzou M; Thornton J M
New tools and resources for analysing protein structures and their interactions.
Acta crystallographica. Section D, Biological crystallography 1998;54(Pt 6 Pt 1):1132-8.
-
1998: Swindells M B; Orengo C A; Jones D T; Hutchinson E G; Thornton J M
Contemporary approaches to protein structure classification.
BioEssays : news and reviews in molecular, cellular and developmental biology 1998;20(11):884-91.
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1998: Hutchinson E G; Sessions R B; Thornton J M; Woolfson D N
Determinants of strand register in antiparallel beta-sheets of proteins.
Protein science : a publication of the Protein Society 1998;7(11):2287-300.
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1998: Milburn D; Laskowski R A; Thornton J M
Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Protein engineering 1998;11(10):855-9.
-
1998: Laskowski R A; MacArthur M W; Thornton J M
Validation of protein models derived from experiment.
Current opinion in structural biology 1998;8(5):631-9.
-
1998: Henrick K; Thornton J M
PQS: a protein quaternary structure file server.
Trends in biochemical sciences 1998;23(9):358-61.
-
1998: Westhead D R; Thornton J M
Protein structure prediction.
Current opinion in biotechnology 1998;9(4):383-9.
-
1998: Bloch C; Patel S U; Baud F; Zvelebil M J; Carr M D; Sadler P J; Thornton J M
1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.
Proteins 1998;32(3):334-49.
-
1998: Martin A C; Orengo C A; Hutchinson E G; Jones S; Karmirantzou M; Laskowski R A; Mitchell J B; Taroni C; Thornton J M
Protein folds and functions.
Structure (London, England : 1993) 1998;6(7):875-84.
-
1998: Viles J H; Patel S U; Mitchell J B; Moody C M; Justice D E; Uppenbrink J; Doyle P M; Harris C J; Sadler P J; Thornton J M
Design, synthesis and structure of a zinc finger with an artificial beta-turn.
Journal of molecular biology 1998;279(4):973-86.
-
1998: Jones S; Stewart M; Michie A; Swindells M B; Orengo C; Thornton J M
Domain assignment for protein structures using a consensus approach: characterization and analysis.
Protein science : a publication of the Protein Society 1998;7(2):233-42.
-
1998: Westhead D R; Hatton D C; Thornton J M
An atlas of protein topology cartoons available on the World-Wide Web.
Trends in biochemical sciences 1998;23(1):35-6.
-
1998: Patel S U; Osborn R; Rees S; Thornton J M
Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).
Biochemistry 1998;37(4):983-90.
-
1997: Laskowski R A; Hutchinson E G; Michie A D; Wallace A C; Jones M L; Thornton J M
PDBsum: a Web-based database of summaries and analyses of all PDB structures.
Trends in biochemical sciences 1997;22(12):488-90.
-
1997: Luscombe N M; Laskowski R A; Thornton J M
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Nucleic acids research 1997;25(24):4940-5.
-
1997: Wallace A C; Borkakoti N; Thornton J M
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 1997;6(11):2308-23.
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1997: Mitchell J B; Laskowski R A; Thornton J M
Non-randomness in side-chain packing: the distribution of interplanar angles.
Proteins 1997;29(3):370-80.
-
1997: Jones S; Thornton J M
Prediction of protein-protein interaction sites using patch analysis.
Journal of molecular biology 1997;272(1):133-43.
-
1997: Jones S; Thornton J M
Analysis of protein-protein interaction sites using surface patches.
Journal of molecular biology 1997;272(1):121-32.
-
1997: Williams M A; Thornton J M; Goodfellow J M
Modelling protein unfolding: hen egg-white lysozyme.
Protein engineering 1997;10(8):895-903.
-
1997: Orengo C A; Michie A D; Jones S; Jones D T; Swindells M B; Thornton J M
CATH--a hierarchic classification of protein domain structures.
Structure (London, England : 1993) 1997;5(8):1093-108.
-
1997: Martin A C; MacArthur M W; Thornton J M
Assessment of comparative modeling in CASP2.
Proteins 1997;Suppl 1():14-28.
-
1996: Laskowski R A; Rullmannn J A; MacArthur M W; Kaptein R; Thornton J M
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Journal of biomolecular NMR 1996;8(4):477-86.
-
1996: MacArthur M W; Thornton J M
Deviations from planarity of the peptide bond in peptides and proteins.
Journal of molecular biology 1996;264(5):1180-95.
-
1996: Laskowski R A; Luscombe N M; Swindells M B; Thornton J M
Protein clefts in molecular recognition and function.
Protein science : a publication of the Protein Society 1996;5(12):2438-52.
-
1996: Viles J H; Mitchell J B; Gough S L; Doyle P M; Harris C J; Sadler P J; Thornton J M
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 1996;242(2):352-62.
-
1996: Martin A C; Thornton J M
Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.
Journal of molecular biology 1996;263(5):800-15.
-
1996: Moodie S L; Mitchell J B; Thornton J M
Protein recognition of adenylate: an example of a fuzzy recognition template.
Journal of molecular biology 1996;263(3):486-500.
-
1996: MacCallum R M; Martin A C; Thornton J M
Antibody-antigen interactions: contact analysis and binding site topography.
Journal of molecular biology 1996;262(5):732-45.
-
1996: Michie A D; Orengo C A; Thornton J M
Analysis of domain structural class using an automated class assignment protocol.
Journal of molecular biology 1996;262(2):168-85.
-
1996: Wallace A C; Laskowski R A; Thornton J M
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 1996;5(6):1001-13.
-
1996: Laskowski R A; Thornton J M; 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 1996;259(1):175-201.
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1996: Jones D T; Moody C M; Uppenbrink J; Viles J H; Doyle P M; Harris C J; Pearl L H; Sadler P J; Thornton J M
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 1996;24(4):502-13.
-
1996: Kalsi J K; Martin A C; Hirabayashi Y; Ehrenstein M; Longhurst C M; Ravirajan C; Zvelebil M; Stollar B D; Thornton J M; Isenberg D A
Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.
Molecular immunology 1996;33(4-5):471-83.
-
1996: Hutchinson E G; Thornton J M
PROMOTIF--a program to identify and analyze structural motifs in proteins.
Protein science : a publication of the Protein Society 1996;5(2):212-20.
-
1996: Wallace A C; Laskowski R A; Singh J; Thornton J M
Molecular recognition by proteins: protein-ligand interactions from a structural perspective.
Biochemical Society transactions 1996;24(1):280-4.
-
1996: Miller R T; Jones D T; Thornton J M
Protein fold recognition by sequence threading: tools and assessment techniques.
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1996;10(1):171-8.
-
1995: Martin A C; Toda K; Stirk H J; Thornton J M
Long loops in proteins.
Protein engineering 1995;8(11):1093-101.
-
1995: Jones D T; Miller R T; Thornton J M
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Proteins 1995;23(3):387-97.
-
1995: Orengo C A; Swindells M B; Michie A D; Zvelebil M J; Driscoll P C; Waterfield M D; Thornton J M
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 1995;4(10):1977-83.
-
1995: Swindells M B; MacArthur M W; Thornton J M
Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.
Nature structural biology 1995;2(7):596-603.
-
1995: Thornton J M; Jones D T; MacArthur M W; Orengo C M; Swindells M B
Protein folds: towards understanding folding from inspection of native structures.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1995;348(1323):71-9.
-
1995: McDonald I K; Thornton J M
The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains.
Protein engineering 1995;8(3):217-24.
-
1995: Wallace A C; Laskowski R A; Thornton J M
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Protein engineering 1995;8(2):127-34.
-
1994: Hutchinson E G; Thornton J M
A revised set of potentials for beta-turn formation in proteins.
Protein science : a publication of the Protein Society 1994;3(12):2207-16.
-
1994: Williams M A; Goodfellow J M; Thornton J M
Buried waters and internal cavities in monomeric proteins.
Protein science : a publication of the Protein Society 1994;3(8):1224-35.
-
1994: Mitchell J B; Nandi C L; McDonald I K; Thornton J M; Price S L
Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
Journal of molecular biology 1994;239(2):315-31.
-
1994: McDonald I K; Thornton J M
Satisfying hydrogen bonding potential in proteins.
Journal of molecular biology 1994;238(5):777-93.
-
1994: MacArthur M W; Driscoll P C; Thornton J M
NMR and crystallography--complementary approaches to structure determination.
Trends in biotechnology 1994;12(5):149-53.
-
1994: Hubbard S J; Eisenmenger F; Thornton J M
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Protein science : a publication of the Protein Society 1994;3(5):757-68.
-
1994: Jones D T; Taylor W R; Thornton J M
A model recognition approach to the prediction of all-helical membrane protein structure and topology.
Biochemistry 1994;33(10):3038-49.
-
1994: Jones D T; Taylor W R; Thornton J M
A mutation data matrix for transmembrane proteins.
FEBS letters 1994;339(3):269-75.
-
1994: Flores T P; Moss D S; Thornton J M
An algorithm for automatically generating protein topology cartoons.
Protein engineering 1994;7(1):31-7.
-
1994: Stirk H J; Thornton J M
The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.
Protein engineering 1994;7(1):47-56.
-
1993: MacArthur M W; Thornton J M
Conformational analysis of protein structures derived from NMR data.
Proteins 1993;17(3):232-51.
-
1993: Flores T P; Orengo C A; Moss D S; Thornton J M
Comparison of conformational characteristics in structurally similar protein pairs.
Protein science : a publication of the Protein Society 1993;2(11):1811-26.
-
1993: Chan A W; Hutchinson E G; Harris D; Thornton J M
Identification, classification, and analysis of beta-bulges in proteins.
Protein science : a publication of the Protein Society 1993;2(10):1574-90.
-
1993: Orengo C A; Thornton J M
Alpha plus beta folds revisited: some favoured motifs.
Structure (London, England : 1993) 1993;1(2):105-20.
-
1993: Orengo C A; Flores T P; Taylor W R; Thornton J M
Identification and classification of protein fold families.
Protein engineering 1993;6(5):485-500.
-
1993: Woolfson D N; Evans P A; Hutchinson E G; Thornton J M
Topological and stereochemical restrictions in beta-sandwich protein structures.
Protein engineering 1993;6(5):461-70.
-
1993: Laskowski R A; Moss D S; Thornton J M
Main-chain bond lengths and bond angles in protein structures.
Journal of molecular biology 1993;231(4):1049-67.
-
1993: Nandi C L; Singh J; Thornton J M
Atomic environments of arginine side chains in proteins.
Protein engineering 1993;6(3):247-59.
-
1993: Hutchinson E G; Thornton J M
The Greek key motif: extraction, classification and analysis.
Protein engineering 1993;6(3):233-45.
-
1993: Orengo C A; Flores T P; Jones D T; Taylor W R; Thornton J M
Recurring structural motifs in proteins with different functions.
Current biology : CB 1993;3(3):131-9.
-
1993: Moodie S L; Thornton J M
A study into the effects of protein binding on nucleotide conformation.
Nucleic acids research 1993;21(6):1369-80.
-
1993: Sibanda B L; Thornton J M
Accommodating sequence changes in beta-hairpins in proteins.
Journal of molecular biology 1993;229(2):428-47.
-
1992: Stirk H J; Woolfson D N; Hutchinson E G; Thornton J M
Depicting topology and handedness in jellyroll structures.
FEBS letters 1992;308(1):1-3.
-
1992: Mitchell J B; Thornton J M; Singh J; Price S L
Towards an understanding of the arginine-aspartate interaction.
Journal of molecular biology 1992;226(1):251-62.
-
1992: Morris A L; MacArthur M W; Hutchinson E G; Thornton J M
Stereochemical quality of protein structure coordinates.
Proteins 1992;12(4):345-64.
-
1992: Stirk H J; Thornton J M; Howard C R
A topological model for hepatitis B surface antigen.
Intervirology 1992;33(3):148-58.
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1992: Hubbard S J; Thornton J M; Campbell S F
Substrate recognition by proteinases.
Faraday discussions 1992;(93):13-23.
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1991: Thanki N; Umrania Y; Thornton J M; Goodfellow J M
Analysis of protein main-chain solvation as a function of secondary structure.
Journal of molecular biology 1991;221(2):669-91.
-
1991: Swindells M B; Thornton J M
Structure prediction and modelling.
Current opinion in biotechnology 1991;2(4):512-9.
-
1991: Hubbard S J; Campbell S F; Thornton J M
Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors.
Journal of molecular biology 1991;220(2):507-30.
-
1991: MacArthur M W; Thornton J M
Influence of proline residues on protein conformation.
Journal of molecular biology 1991;218(2):397-412.
-
1991: Garratt R C; Thornton J M; Taylor W R
An extension of secondary structure prediction towards the prediction of tertiary structure.
FEBS letters 1991;280(1):141-6.
-
1991: Singh J; Saldanha J; Thornton J M
A novel method for the modelling of peptide ligands to their receptors.
Protein engineering 1991;4(3):251-61.
-
1991: Thornton J M
Modelling antibody combining sites: a review.
Ciba Foundation symposium 1991;159():55-69; discussion 69-71.
-
1990: Wilmot C M; Thornton J M
Beta-turns and their distortions: a proposed new nomenclature.
Protein engineering 1990;3(6):479-93.
-
1990: Thanki N; Thornton J M; Goodfellow J M
Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins.
Protein engineering 1990;3(6):495-508.
-
1990: Singh J; Thornton J M
SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups.
Journal of molecular biology 1990;211(3):595-615.
-
1990: Hutchinson E G; Thornton J M
HERA--a program to draw schematic diagrams of protein secondary structures.
Proteins 1990;8(3):203-12.
-
1989: Sibanda B L; Blundell T L; Thornton J M
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 1989;206(4):759-77.
-
1989: Reid L S; Thornton J M
Rebuilding flavodoxin from C alpha coordinates: a test study.
Proteins 1989;5(2):170-82.
-
1988: Thornton J M; Singh J; Campbell S; Blundell T L
Protein-protein recognition via side-chain interactions.
Biochemical Society transactions 1988;16(6):927-30.
-
1988: Wilmot C M; Thornton J M
Analysis and prediction of the different types of beta-turn in proteins.
Journal of molecular biology 1988;203(1):221-32.
-
1988: Thanki N; Thornton J M; Goodfellow J M
Distributions of water around amino acid residues in proteins.
Journal of molecular biology 1988;202(3):637-57.
-
1988: Barlow D J; Thornton J M
Helix geometry in proteins.
Journal of molecular biology 1988;201(3):601-19.
-
1987: Singh J; Thornton J M; Snarey M; Campbell S F
The geometries of interacting arginine-carboxyls in proteins.
FEBS letters 1987;224(1):161-71.
-
1987: Edwards M S; Sternberg J E; Thornton J M
Structural and sequence patterns in the loops of beta alpha beta units.
Protein engineering 1987;1(3):173-81.
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