Thornton Group Publications

The following is a list of publications for the Thornton group.

2012
2011
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
1991-2000

2012

Ballester PJ & Brown N, (2012)

Bioisosteres in Medicinal Chemistry (Methods and Principles in Medicinal Chemistry)

Wiley-VCH

Amazon

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2011

Alic,N.; Andrews,T. D.; Giannakou,M. E.; Papatheodorou,I.; Slack,C.; Hoddinott,M. P.; Cocheme,H. M.; Schuster,E. F.; THORNTON,J. M.; Partridge,L. (2011)

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

Molecular systems biology Jun 21 7 502

PMID: 21694719 DOI: 10.1038/msb.2011.36

Partridge,L.; THORNTON,J. M.; Bates,G. (2011)

The new science of ageing

Philos.Trans.R.Soc.Lond.B.Biol.Sci. Jan 12 366 1561 6

PMID: 21115524 DOI: 10.1098/rstb.2010.0298

THORNTON,J. M. (2011)

Celebrating structural biology:Abstracting knowledge from the PDB over 40 years

Nature structural & molecular biology Dec 5 18 12 1304

PMID: 22139036 DOI: 10.1038/nsmb1211-1304

Cuff,A. L.; Sillitoe,I.; Lewis,T.; Clegg,A. B.; Rentzsch,R.; FURNHAM,N.; Pellegrini-Calace,M.; Jones,D.; THORNTON,J.; Orengo,C. A. (2011)

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

Nucleic acids research 39 D420

PMID: 21097779 DOI: 10.1093/nar/gkq1001

ORCHARD,S.; Al-Lazikani,B.; Bryant,S.; CLARK,D.; Calder,E.; Dix,I.; Engkvist,O.; Forster,M.; GAULTON,A.; Gilson,M.; Glen,R.; Grigorov,M.; Hammond-Kosack,K.; Harland,L.; Hopkins,A.; Larminie,C.; Lynch,N.; Mann,R. K.; Murray-Rust,P.; Lo Piparo,E.; Southan,C.; STEINBECK,C.; Wishart,D.; HERMJAKOB,H.; OVERINGTON,J.; THORNTON,J. (2011)

Minimum information about a bioactive entity (MIABE)

Nature reviews Drug discovery Aug 31 10 9 661

PMID: 21878981 DOI: 10.1038/nrd3503

Ballester PJ & Mitchell JBO (2011)

Comments on "Leave-Cluster-Out Cross-Validation is appropriate for scoring functions derived from diverse protein data sets": significance for the validation of scoring functions

Journal of Chemical Information and Modeling 51(8), 1739–1741

DOI: 10.1021/ci200057e

McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P & Köhn (2011)

The Metastasis-Promoting Phosphatase PRL-3 Shows Activity toward Phosphoinositides

Biochemistry Sep 6;50(35):7579-7590

DOI: 10.1021/bi201095z

Holliday GL, Fischer JD, Mitchell JBO, Thornton JM (2011)

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

FEBS J 278 (20), 3835-3845

DOI: 10.1111/j.1742-4658.2011.08190.x

Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST (2011)

MACiE: Exploring the diversity of biochemical reactions.

Nucleic Acids Res.Nucl. Acids Res. (2011)

DOI: 10.1093/nar/gkr799

Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM (2011)

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

Nucleic Acids Res. October 17,

PMID: 10.1093/nar/gkr852

Ballester, P.J. (2011)

Ultrafast Shape Recognition: Method and Applications.

Future Medicinal Chemistry Vol. 3 (1) 65-78.

Lee D, de Beer T A P, Laskowski R A, Thornton J M, Orengo C A (2011)

1,000 structures and more from the MCSG.

BMC Structural Biology, 11:2.

PMID: 21219649

Laskowski R A (2011)

Protein structure databases.

Molecular Biotechnology, in press.

Wieser, D., Papatheodorou, I., Ziehm, M., Thornton, J.M. (2011)

Computational biology for ageing.

Philos Trans R Soc Lond B Biol Sci. 366(1561): 51-63.

PMID: 21115530

2010

Bashton, M., Thornton, J.M. (2010)

Domain-Ligand Mapping for Enzymes.

Journal of Molecular Recognition 23, no. 2 (2010): 194-208.

PMID: 19810051

Grönke, S., Clarke, D.F., Broughton, S., Andrews T.D., Partridge, L. (2010)

Molecular Evolution and Functional Characterization of Drosophila Insulin-Like Peptides.

PLoS Genetics 6, no. 2 (2010).

PMID: 20195512

Talavera, D., Taylor M.S., Thornton, J.M. (2010)

The (Non)Malignancy of Cancerous Amino Acidic Substitutions.

Proteins: Structure, Function and Bioformatics 78, no. 3 (2010): 518-29.

PMID: 19787769

Ballester P.J., Mitchell J.B.O. (2010).

A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

Bioinformatics 26 (2010): 1169-1175

PMID: 20236947

Ballester P.J., Westwood I., Laurieri N., Sim E. and Richards W.G. (2010)

Prospective Virtual Screening with Ultrafast Shape Recognition: The Identification of Novel Inhibitors of Arylamine N-acetyltransferases

Journal of the Royal Society Interface, 7, (2010): 335-342

PMID: 19586957

Berka K., Laskowski R., Hobza P., Vondrasek J. (2010).

Energy matrix of structurally important side-chain/side-chain interactions in proteins.

J. Chem. Theory Comput., 6, 2191-2203.

Brooksbank C., Cameron G., Thornton J. (2010)

The European Bioinformatics Institute’s data resources.

Nucleic Acids Research 38: D17-D25.

PMID: 19934258

Chan A.W.E., Laskowski R.A., Selwood D. (2010).

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.

J. Med. Chem., 53, 3086-3094.

PMID: 20230000

Fischer J.D., Holliday G.L., Rahman S. A., Thornton J.M. (2010).

The structures and physicochemical properties of organic cofactors in biocatalysis.

Journal of Molecular Biology, 403(5), 12 November 2010, Pages 803-824, ISSN 0022-2836, DOI: 10.1016/j.jmb.2010.09.018.

PMID: 20850456

Fischer J.D., Holliday G.L., Thornton J.M. (2010).

The CoFactor database: Organic cofactors in enzyme catalysis. Bioinformatics.

PMID: 20679331

Laskowski R.A. (2010).

Protein structure databases,

in Data Mining Techniques for the Life Sciences, Methods in Molecular Biology 609,,eds. Carugo O & Eisenhaber F, Humana Press, New York, 59-82.

PMID: 20221913

Kahraman A., Morris R.J., Laskowski R.A., Favia A.D., Thornton J.M. (2010).

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

Proteins, 78, 1120-1136.

PMID: 19927322

O'Donoghue S.I., Goodsell D.S., Frangakis A.S., Jossinet F., Laskowski R.A., Nilges M., Saibil H.R., Schafferhans A., Wade R.C., Westhof E., Olson A.J. (2010).

Visualization of macromolecular structures.

Nat. Meth., 7, S42-S55.

Oliva R., Calamita G. Thornton J.M. & Pellegrini-Calace M. (2010)

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity

PNAS, in press.

Schuster E., McElwee J.J., Tullet J.M.A., Doonan R., Matthijssens F., Reece-Hoyes J.S., Hope I.A., Vanfleteren J.R., Thornton J.M., Gems D. (2010)

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

Citation: Molecular Systems Biology 6:399

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Slack C., Werz C., Wieser D., Alic N., Foley A., Stocker H, Withers D.J., Thornton J.M., Hafen E., Partridge L. (2010)

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

2010 March; Plos Genetics

PMID: 20333234

Smith L.J., Kahraman A., Thornton J.M. (2010).

Heme proteins--diversity in structural characteristics, function, and folding. Proteins.

2010 Aug 1;78(10):2349-68.

Tamuri A.U., Laskowski R.A. (2010).

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.

Bioinformatics, 26, 1260-1261.

PMID: 20299327

2009

Cuff, A., Redfern, O.C., Greene, L., Sillitoe, I., Lewis, T., Dibley, M., Reid, A., Pearl, F., Dallman, T., Todd, A., Garratt, R., Thornton, J., Orengo, C. (2009)

The Cath Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space.

Structure 17, no. 8 (2009): 1051-62.

PMID: 19679085

Herrera, J.L., Gonzalez-Rey, E., Fernandez-Montesinos, R., Quintana, F.J., Najmanovich, R., Pozo, D. (2009)

Toll-Like Receptor Stimulation Differentially Regulates Vasoactive Intestinal Peptide Type 2 Receptor in Macrophages.

Journal of Cellular and Molecular Medicine 13, no. 9 B (2009): 3209-17.

Laskowski, R. (2009)

Integrated Servers for Structure-Informed Function Prediction.

In Protein Structure to Function with Bioinformatics,, edited by Rigden D J, 251-72: Springer, 2009.

Laskowski, R. (2009)

Structural Quality Assurance.

In Structural Bioinformatics, edited by Gu J & Bourne P E, 341-75. New Jersey: John Wiley, 2009.

Macchiarulo, A., Thornton J.M., Nobeli, I. (2009)

Mapping Human Metabolic Pathways in the Small Molecule Chemical Space.

Journal of Chemical Information and Modeling 49, no. 10 (2009): 2272-89.

Toronto International Data Release Workshop, Authors, Birney, E., Hudson, T.J., Green, E.D., Gunter, C., Eddy, S., Rogers, J., Harris, J.R., Ehrlich, S.D., Apweiler, R., Austin, C.P., Berglund, L., Bobrow, M., Bountra, C., Brookes, A.J., Cambon-Thomsen, A., Carter, N.P., Chisholm, R.L., Contreras, J.L., Cooke, R.M., Crosby, W.L., Dewar, K., Durbin, R., Dyke, S.O., Ecker, J.R., El Emam. K., Feuk, L., Gabriel, S.B., Gallacher, J., Gelbart, W.M., Granell, A., Guarner, F., Hubbard, T., Jackson, S.A., Jennings, J.L., Joly, Y., Jones, S.M., Kaye, J., Kennedy, K.L., Knoppers, B.M., Kyrpides, N.C., Lowrance, W.W., Luo, J., MacKay, J.J., Martin-Rivera, L., McCombie, W.R., McPherson, J.D., Miller, L., Miller, W., Moerman, D., Mooser, V., Morton, C.C., Ostell, J.M., Ouellette, B.F., Parkhill, J., Raina, P.S., Rawlings, C., Scherer, S.E., Scherer, S.W., Schofield, P.N., Sensen, C.W., Stodden, V.C., Sussman, M.R., Tanaka, T., Thornton, J., Tsunoda, T., Valle, D., Vuorio, E.I., Walker, N.M., Wallace, S., Weinstock, G., Whitman, W.B., Worley, K.C., Wu, C., Wu, J., Yu, J. (2009)

Prepublication Data Sharing.

Nature 461, no. 7261 (2009): 168-70.

Wieser, D., Niranjan, M. (2009)

Remote Homology Detection Using a Kernel Method That Combines Sequence and Secondary-Structure Similarity Scores.

In Silico Biology 9, no. 3 (2009): 89-103.

Andreini, I. Bertini, G. Cavallaro, G. L. Holliday and Thornton J.M. (2009)

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

Bioinformatics 25: 2088-2089.

PMID: 19369503

Berka K., Laskowski R., Riley K.E., Hobza P., Vondrasek J. (2009).

Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures.

Journal of Chemical Theory and Computation 5(4): 982-992.

Abstract: DOI: 10.1021/ct800508v

Blum A., Favia A.D., Maser E. (2009)

11 beta-Hydroxysteroid dehydrogenase type 1 inhibitors with oleanan and ursan scaffolds.

Molecular and Cellular Endocrinology 301(1-2): 132-136.

PMID: 18822345

Capra J.A., Laskowski R.A., Thornton J.M., Singh M., Funkhouser T.A. (2009).

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

PLoS Comput Biol., 5, e1000585.

PMID: 19997483

El-Hawari Y., Favia A.D., Pilka E.S., Kisiela M., Oppermann U., Martin H.J., Maser E. (2009)

Analysis of the substrate-binding site of human carbonyl reductases CBR1 and CBR3 by site-directed mutagenesis.

Chemico-Biological Interactions 178(1-3): 234-241.

PMID: 19061875

Furnham N., Garavelli J.S., Apweiler R., Thornton J.M. (2009)

Missing in action: enzyme functional annotations in biological databases.

Nature Chemical Biology 2009 Aug;5(8): 521-525.

PMID: 19620987

Holliday G.L., Mitchell J.B.O. and Thornton J.M. (2009)

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

Journal of Molecular Biology 390: 560-577.

PMID: 19447117

Laskowski R.A. (2009)

PDBsum new things.

Nucleic Acids Research 37: D355-D359.

PMID: 18996896

Laskowski R.A., Gerick F., Thornton J.M. (2009)

The structural basis of allosteric regulation in proteins.

FEBS Letters 583: 1692-1698.

PMID: 19303011

Laskowski R.A., Thornton J.M., Sternberg M.J. (2009).

The fine details of evolution.

Biochemical Society Transactions 37: 723-726.

PMID: 19614583

Nobeli I., Favia A.D., Thornton J.M. (2009)

Protein promiscuity and its implications for biotechnology.

Nature Biotechnology 27(2): 157-167.

PMID: 19204698

Oliva R., Thornton J.M. & Pellegrini-Calace M. (2009)

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

Bioinformatics 25, 3183-3184.

PMID: 19762348

Pellegrini-Calace M., Maiwald T., Thornton J.M. (2009)

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.

PLoS Computatinal Biology, 5(7): e1000440. doi:10.1371/journal.pcbi.1000440

PMID: 19609355

Persson B., Bray J.E., Bruford E., Dellaporta S.L., Favia A.D., Duarte R.G., Jörnvall H., Kallberg Y., Kavanagh K.L., Kedishvili N., Kisiela M., Maser E., Mindnich R., Orchard S., Penning T.M., Thornton J.M., Adamski J., Oppermann U. (2009)

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

Chemico-Biological Interactions 178(1-3): 94-98.

PMID: 19027726

Rahman S.A., Bashton M., Holliday G.L., Schrader R. and Thornton J.M. (2009)

Small Molecule Subgraph Detector (SMSD) toolkit.

Journal of Cheminformatics 2009, 1:12.

Abstract: DOI:10.1186/1758

Reeves G.A., Talavera D., Thornton J.M (2009)

Genome and Proteome Annotation: Organisation, Interpretation and Integration.

Journal of the Royal Society Interface 6(31): 129-147.

PMID: 19019817

Selman C., Tullet J.M., Wieser D., Irvine E., Lingard S.J., Choudhury A.I., Claret M., Al-Qassab H., Carmignac D., Ramadani F., Woods A., Robinson I.C., Schuster E., Batterham R.L., Kosma S.C., Thomas G., Carling D., Okkenhaug K., Thornton J.M., Partridge L., Gems D. and Withers D.J. (2009).

Ribosomal S6 kinase 1 signaling regulates mammalian life span.

Science. 326: 140-4.

PMID: 19797661

Soranzo N., Spector T.D., Mangino M., Kühnel B., Rendon A., Teumer A., Willenborg C., Wright B., Chen L., Li M., Salo P., Voight B.F., Burns P., Laskowski R.A., Xue Y., Menzel S., Altshuler D., Bradley J.R., Bumpstead S., Burnett M.S., Devaney J., Döring A., Elosua R., Epstein S.E., Erber W., Falchi M., Garner S.F., Ghori M.J., Goodall A.H., Gwilliam R., Hakonarson H.H., Hall A.S., Hammond N., Hengstenberg C., Illig T., König I.R., Knouff C.W., McPherson R., Melander O., Mooser V., Nauck M., Nieminen M.S., O'Donnell C.J., Peltonen L., Potter S.C., Prokisch H., Rader D.J., Rice C.M., Roberts R., Salomaa V., Sambrook J., Schreiber S., Schunkert H., Schwartz S.M., Serbanovic-Canic J., Sinisalo J., Siscovick D.S., Stark K., Surakka I., Stephens J., Thompson J.R., Völker U., Völzke H., Watkins N.A., Wells G.A., Wichmann H.E., Van Heel D.A., Tyler-Smith C., Thein S.L., Kathiresan S., Perola M., Reilly M.P., Stewart A.F., Erdmann J., Samani N.J., Meisinger C., Greinacher A., Deloukas P., Ouwehand W.H., Gieger C. (2009).

A meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.

Nature Genetics, 41, 1182-1190.

PMID: 19820697

Talavera D., Laskowski R.A., Thornton J.M. (2009)

WSsas: a web service for the annotation of functional residues through structural homologues.

Bioinformatics 25: 1192-1194.

PMID: 19251774

Talavera D., Orozco M., de la Cruz X. (2009)

Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity.

Comparative and Functional Genomics 2009: 905894. Epub 2009 Jul 12.

PMID: 19609452

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2008

Andreini C, Bertini I, Cavallaro G, Holliday G.L, Thornton J.M. (2008)

Metal ions in biological catalysis: From enzyme databases to general principles.

Journal of Biological Inorganic Chemistry 13: 1205-1218

PMID: 18604568

Bashton M., Nobeli I., Thornton J.M. (2008)

PROCOGNATE: a cognate ligand domain mapping for enzymes.

Nucleic Acids Research 36(Database issue): D618-D622.

PMID: 17720712

Bavro V.N., Pietras Z., Furnham N., P.rez-Cano L., Fern.ndez-Recio J., Pei X.Y., Misra R., Luisi B. (2008)

Assembly and channel opening in a bacterial drug efflux machine.

Molecular Cell. 30(1):114-21.

PMID: 18406332

Eswaran J., Bernad A., Ligos J.M., Barbara Guinea, Debreczeni J. É., Sobott F., Parker S. A., Najmanovich R., Turk B. E. and Knapp S. (2008)

Structure of the Human Protein Kinase MPSK1 Reveals an Atypical Activation Loop Architecture

Structure 16(1): 115-124

Favia A.D., Nobeli I., Glaser F., Thornton J.M. (2008)

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

Journal of Molecular Biology 375(3): 855-874.

PMID: 18036612

Freilich S., Goldovsky L., Ouzounis C.A., Thornton J.M. (2008)

Metabolic innovations towards the human lineage.

BMC Evol Biol. 8(1):247.

PMID: 18782449

Furnham N., de Bakker P.I., Gore S., Burke D.F., Blundell T.L. (2008)

Comparative modelling by restraint-based conformational sampling.

BMC Structural Biology. 8:7.

PMID: 18237407

Herrera J.L., Fernandez-Montesinos R., Quintana F.J., Najmanovich R., Gonzalez-Rey E., Pozo D. (2008)

Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages.

Journal of Cellular and Molecular Medicine (in press).

Jenkinson A. M., Albrecht M., Birney E., Blankenburg H., Down T., Finn R. D., Hermjakob H., Hubbard T. J. P., Jiminez R. C., Jones P., Kahari A., Kulesha E., Macias J. R., Reeves G. A. and Prlic A. (2008)

Integrating Biological Data – the Distributed Annotation System.

BMC Bioinformatics 9, no. SUPPL. 8 (2008): Article S3.

Kahraman A. & Thornton J.M. (2008)

Methods to Characterize the Structure of Enzyme Binding Sites.

In Computational Structural Biology - Methods and Applications - (Schwede, T. & Peitsch, M. C., eds.), Vol. 1, pp. 189-221. 1 vols. World Scientific Publishing Co.

Laskowski R., A. & Thornton J. M. (2008)

Understanding the molecular machinery of genetics through 3D structures.

Nature Reviews Genetics 9(2): 141-151.

PMID: 18160966

Najmanovich R., Kurbatova N. & Thornton J. (2008)

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

Bioinformatics 24(18): i105-i111.

PMID: 18689810

Patel P., Harris R., Geddes S.M., Strehle E.M., Watson J.D., Bashir R., Bushby K., Driscoll P.C., Keep N.H. (2008)

Solution structure of the inner DysF domain of myoferlin and implications for limb girdle muscular dystrophy type 2b.

J Mol Biol. 379(5):981-90.

Pietras Z., Bavro V.N., Furnham N., Pellegrini-Calace M., Milner-White E.J., Luisi B.F. (2008)

Structure and mechanism of drug efflux machinery in Gram negative bacteria.

Current Drug Targets. 9(9):719-28.

PMID: 18781919

Ragone S., Maman J.D., Furnham N., Pellegrini L. (2008)

Structural basis for inhibition of homologous recombination by the RecX protein.

EMBO Journal 27(16):2259-69. Epub.

PMID: 18650935

Reeves G. A., Eilbeck K., Magrane M., O'Donovan C., Montecchi-Palazzi L., Harris M. A., Orchard S., Jimenez R. C., Prlic A., Hubbard T. J. P., Hermjakob H. and Thornton J. M. (2008)

The Protein Feature Ontology: A Tool for the Unification of Protein Feature Annotations.

Bioinformatics 24, no. 23: 2767-72.

Selman, C., Lingard S., Choudhury A. I., Batterham R. L., Claret M., Clements M., Ramadani F., Okkenhaug K., Schuster E., Blanc E., Piper M. D., Al-Qassab H., Speakman J. R., Carmignac D., Robinson I. C. A., Thornton J. M., Gems D., Partridge L. and Withers D. J. (2008)

Evidence for Lifespan Extension and Delayed Age-Related Biomarkers in Insulin Receptor Substrate 1 Null Mice.

FASEB Journal 22, no. 3: 807-18.

Torrance, J. W., MacArthur M. W. and Thornton J. M. (2008)

Evolution of Binding Sites for Zinc and Calcium Ions Playing Structural Roles.

Proteins: Structure, Function and Genetics 71, no. 2: 813-30.

Thornton J.M., Favia A.D., Nobeli I. and Furnham N. (2008)

The evolution of specificity in large protein families.

FEBS Journal 275: 23-23.

Top

2007

Allali-Hassani, A., Pan P. W., Dombrovski L., Najmanovich R., Tempel W., Dong A., Loppnau P., Martin F., Thonton J., Edwards A. M., Bochkarev A., Plotnikov A. N., Vedadi M. and Arrowsmith C. H. (2007)

Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases.

PLoS Biology 5, no. 5: 1063-78.

Bashton M., Chothia C. (2007)

The generation of new protein functions by the combination of domains.

Structure 2007 Jan;15(1): 85-99.

PMID: 17223535

Cuff M. E., Li H., Moy S., Watson J., Cipriani A., Joachimiak A. (2007)

Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961.

Proteins 69(2): 422-427.

PMID: 17623843

Freeman, T. C., Goldovsky L., Brosch M., Van Dongen S., Maziere P., Grocock R. J., Freilich S., Thornton J. and Enright A. J. (2007)

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

PLoS Computational Biology 3, no. 10: 2032-42.

Greene L. H., Lewis T. E., Addou S., Cuff A., Dallman T., Dibley M., Redfern O., Pearl F., Nambudiry R., Reid A., Sillitoe I., Yeats C., Thornton J. M., Orengo C. A. (2007)

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

Nucleic Acids Research 35: D291-297.

PMID: 17135200

Holliday G. L., Almonacid D. E., Bartlett G. J., O'Boyle N. M., Torrance J. W., Murray-Rust P., Mitchell J. B., Thornton J. M. (2007)

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

Nucleic Acids Research 35: D515-D520. [Epub 2006 Nov 1]

PMID: 17082206

Holliday G. L., Almonacid D. E., Mitchell J. B. O., Thornton J. M. (2007)

The Chemistry of Protein Catalysis.

Journal of Molecular Biology 372: 1261-1277.

PMID: 17727879

Holliday, G. L., Thornton J. M., Marquet A., Smith A. G., Rebeille F., Mendel R., H. L. Schubert, A. D. Lawrence, and M. J. Warren (2007)

Evolution of Enzymes and Pathways for the Biosynthesis of Cofactors.

Natural Product Reports 24, no. 5: 972-87.

Joshua J. McElwee Schuster E. F., Blanc E., Piper M. D., Thomas J. H., Patel D. S., Selman C., Withers D. J., Thornton J. M., Partridge L., Gems D. (2007)

Evolutionary conservation of regulated longevity assurance mechanisms.

Genome Biology 2007 8: R132. [Epub ahead of print]

PMID: 17612391

Kahraman A., Morris R. J., Laskowski R. A. & Thornton J. M. (2007).

Shape variation in protein binding pockets and their ligands.

Molecular Biology 368: 283-301. [Epub 2007 Feb 7]

PMID: 17337005

Kahraman A., Morris R. J., Laskowski R. A. & Thornton J. M. (2007)

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.

BMC Bioinformatics 8, S1.

Laskowski R. A. (2007)

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.

Bioinformatics 23: 1824-1827.

PMID: 17384425

McElwee J.J., Schuster E. F., Blanc E., Piper M. D., Thomas J. H., Patel D. S., Selman C., Withers D. J., Thornton J. M., Partridge L., Gems D. (2007)

Evolutionary conservation of regulated longevity assurance mechanisms.

Genome Biology 2007 8: R132.

PMID: 17612391

Najmanovich R. J., Allali-Hassani A., Morris R. J., Dombrovsky L., Pan P. W., Vedadi M., Plotnikov A. N., Edwards A., Arrowsmith C., Thornton J. M. (2007)

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

Bioinformatics 2007 23: e104-e109.

PMID: 17237076

Najmanovich R., Allali-Hassani A., Pan P. W., Dombrovski L., Tempel W., Dong A., Loppnau P., Martin F., Thornton J., Edwards A. M., Bochkarev A., Plotnikov A. N., Vedadi M., Arrowsmith C. H. (2007)

Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases.

PloS Biology 5(5): e97.

PMID: 17425406

O'Boyle N. M., Holliday G. L., Almonacid D. E., Mitchell J. B. O. (2007).

Using reaction mechanism to measure enzyme similarity.

Journal of Molecular Biology 368: 1484-1499.

PMID: 17400244

Schuster E. F., Blanc E., Partridge L., Thornton J. M. (2007)

Correcting for sequence biases in present/absent calls.

Genome Biology 8: R125. [Epub ahead of print]

PMID: 17594492

Selman C., Lingard S., Choudhury A. I., Batterham R. L., Claret M., Clements M., Ramadani F., Okkenhaug K., Schuster E. F., Blanc E., Piper M. D., Al-Qassab H., Speakman J. R., Carmignac D., Robinson I. C. A., Thornton J. M., Gems D., Partridge L., Withers D. J. (2007)

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

FASEB (accepted)

Torrance J. W., Holliday G. L., Mitchell J. B., Thornton J. M. (2007)

The geometry of interactions between catalytic residues and their substrates.

Journal of Molecular Biology 2007 Jun 15; 369(4): 1140-52. [Epub 2007 Mar 24]

PMID: 17466330

Torrance, J. W., Macarthur M. W. and Thornton J. M. (2007)

Evolution of Binding Sites for Zinc and Calcium Ions Playing Structural Roles.

Proteins.

Tress M. L., Martelli P. L., Frankish A., Reeves G. A., Wesselink J. J., Yeats C., Olason P. L., Albrecht M., Hegyi H., Giorgetti A., Raimondo D., Lagarde J., Laskowski R. A., López G., Sadowski M. I., Watson J. D., Fariselli P., Rossi I., Nagy A., Kai W., Størling Z., Orsini M., Assenov Y., Blankenburg H., Huthmacher C., Ramírez F., Schlicker A., Denoeud F., Jones P., Kerrien S., Orchard S., Antonarakis S. E., Reymond A., Birney E., Brunak S., Casadio R., Guigo R., Harrow J., Hermjakob H., Jones D. T., Lengauer T., Orengo C. A., Patthy L., Thornton J. M., Tramontano A., Valencia A.

The implications of alternative splicing in the ENCODE protein complement.

Proceedings of the National Academy of Sciences of the United States of America (13): 5495-500.

PMID: 17372197

Ward, J. J. and Thornton J. M. (2007)

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

PLoS Computational Biology 3, no. 10: 1993-2002.

Watson J. D., Golovin A., Laskowski R. A., Henrick K., Thornton J. M., Joachimiak A., Edwards A. M. (2007)

Structural bioinformatics: from protein structure to function.

In Evolving Methods for Macromolecular Crystallography eds. Read R J & Sussman J L Springer pp. 165-179.

Watson J. D., Sanderson S., Ezersky A., Savchenko A., Edwards A., Orengo C., Joachimiak A., Laskowski R. A., Thornton J. M. (2007)

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

Journal of Molecular Biology 367: 1511-1522.

PMID: 17316683

Top

2006

Albeck S., Alzari P., Andreini C., Banci L., Berry I. M., Bertini I., Cambillau C., Canard B., Carter L., Cohen S. X., Diprose J. M., Dym O., Esnouf R. M., Felder C., Ferron F., Guillemot F., Hamer R., Ben Jelloul M., Laskowski R. A., Laurent T., Longhi S Lopez R., Luchinat C., Malet H., Mochel T., Morris R. J., Moulinier L., Oinn T., Pajon A., Peleg Y., Perrakis A., Poch O., Prilusky J., Rachedi A., Ripp R., Rosato A., Silman I., Stuart D. I., Sussman J. L., Thierry J. C., Thompson J. D., Thornton J. M., Unger T., Vaughan B., Vranken W., Watson JD., Whamond G., Henrick K. (2006)

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

Acta Crystallographica Section D: Biological Crystallography 2006 Oct;62(Pt 10): 1184-1195.

PMID: 17001095

Bashton M., Nobeli I., Thornton J. M. (2006)

Cognate ligand domain mapping for enzymes.

Journal of Molecular Biology 2006 Dec 8;364(4): 836-852.

PMID: 17034815

Freilich S., Massingham T., Blanc E., Goldovsky L., Thornton J. M. (2006)

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

Genome Biology 2006 Oct 9;7(10): R89 [Epub 2006 Oct 9]

PMID: 17029626

Glaser F., Morris R. J., Najmanovich R. J., Laskowski R. A., Thornton J. M. (2006)

A method for localizing ligand binding pockets in protein structures.

Proteins 2006 62(2): 479-88.

PMID: 16304646

Han J. H., Kerrison N., Chothia C., Teichmann S. A. (2006)

Divergence of interdomain geometry in two-domain proteins.

Structure 2006 May;14(5): 935-945.

PMID: 16698554

Holliday G. L., Almonacid D. E., Bartlett G. J., O'boyle N. M., Torrance J. W., Murray-Rust P., Mitchell J. B., Thornton J. M. (2006)

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

Nucleic Acids Research 2006 Nov 1; [Epub 2006 Nov 1]

PMID: 17082206

Hurwitz N., Pellegrini-Calace M., Jones D. T. (2006)

Towards genome-scale structure prediction for transmembrane proteins.

Philosophical Transactions of the Royal Society B: Biological Sciences 2006 Mar 29;361(1467): 465-475. Review.

PMID: 16524835

Jones D. J., Sternberg M. J. E. & Thornton J. M. (2006)

Bioinformatics:from molecules to systems.

Philosophical Transactions of the Royal Society B: Biological Sciences 361: 389-391.

DOI: 10. 1098/rstb. 2005. 1811

Laskowski R. A., Swaminathan G. J. (2006)

Problems of protein three-dimensional structures.

In Comprehensive Medicinal Chemistry II eds. Taylor J B & Triggle D J Elsevier Oxford Vol. 3 pp. 531-550.

McElwee J. J., Schuster E., Blanc E., Thornton J., Gems D. (2006)

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

Mech Ageing Dev. 2006 May;127(5): 458-472. [Epub 2006 Mar 7]

PMID: 16522328

Milner-White J. E., Watson J. D., Qi G., Hayward S. (2006)

Amyloid formation may involve alpha- to beta sheet interconversion via peptide plane flipping.

Structure 2006 Sep;14(9): 1369-1376.

PMID: 16962968

Nobeli I., Thornton J. M. (2006)

A bioinformatician's view of the metabolome.

Bioessays 2006 May;28(5): 534-545. Review.

PMID: 16615085

Ranea J. A., Sillero A., Thornton J. M., Orengo C. A. (2006)

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

Journal of Molecular Evolution 2006 Oct;63(4): 513-525. [Epub 2006 Oct 4]

PMID: 17021929

Reeves G. A., Dallman T. J., Redfern O. C., Akpor A., Orengo C. A. (2006)

Structural diversity of domain superfamilies in the CATH database.

Journal of Molecular Biology 2006 Jul 14;360(3): 725-741. [Epub 2006 Jun 2]

PMID: 16780872

Reeves G. A. & Thornton J. M. (2006)

Integrating biological data through the genome (Review).

Human Molecular Genetics 15: R81-R87.

PMID: 16651373

Selman C., Kerrison N. D., Cooray A., Piper M. D., Lingard S. J., Barton R. H., Schuster E. F., Blanc E., Gems D., Nicholson J. K., Thornton J. M., Partridge L., Withers D. J. (2006)

Coordinated multi-tissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.

Physiolical Genomics 2006 Aug 1; [Epub ahead of print]

PMID: 16882887

Stockwell G. R., and Thornton J. M. (2006)

Conformational Diversity of Ligands Bound to Proteins.

Journal of Molecular Biology 2006 356(4): 928-944.

PMID: 16405908

Whamond G. S., Thornton J. M. (2006)

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

Journal of Molecular Biology 2006 May 26;359(1): 238-247. [Epub 2006 Mar 29]

PMID: 16616935

Zhang R., Skarina T., Evdokimova E., Edwards A., Savchenko A., Laskowski R., Cuff M., Joachimiak A. (2006)

Structure of SAICAR synthase from Thermotoga maritima at 2.2 Angstroms reveals an unusual covalent dimer.

Acta Crystallography 2006 Apr 1;62(Pt 4): 335-339.

PMID: 16582479

Top

2005

Brooksbank C., Cameron G., and Thornton J. M. (2005)

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

Nucleic Acids Research 2005 33: D46-D53.

PMID: 15608238

Ferrer-Costa C., Shanahah H. P., Jones S. & Thornton J. M. (2005)

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

Bioinformatics 21: 3679-3680.

PMID: 16030074

Freilich S., Spriggs R. V., George R. A., Al-Lazikani B., Swindells M. & Thornton J. M. (2005)

The complement of enzymatic sets in different species.

Journal of Molecular Biology 349(4): 745-763.

PMID: 15896806

Freilich S., Massingham T., Bhattacharyya S., Ponstingl H., Lyons P. A., Freeman T. C. & Thornton J. M. (2005)

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

Genome Biology 6(7): R56. [Epub 2005 Jun 29]

PMID: 15998445

Funkhouser T., Glaser F., Laskowski R., Morris R. J., Najmanovich R., Stockwell G & . Thornton J. M. (2005)

Shape-based classification of bound ligands.

Quantitative Biology Shape Analysis and Wavelets 39-42 Edited by S. Barber P. D. Baxter K. V. Mardia R. E. Wells. Leeds. ISBN 0 85316 243 3

Furmonaviciene R., Sutton B. J., Glaser F., Laughton C. A., Jones N., Sewell H. F. & Shakib F. (2005)

An attempt to define allergen-specific molecular surface features: a bioinformatic approach. Bioinformatics.

Bioinformatics 2005 Dec 1;21(23): 4201-4204. [Epub 2005 Oct 4]

PMID: 16204345

George R. A., Spriggs R. G., Bartlett G. J., Gutteridge A., MacArthur M. W., Porter C. T., Al-Lazikani B., Thornton J. M. & Swindells M. B. (2005)

Effective function annotation through residue conservation.

Proceedings of the National Academy of Sciences 102: 12299-12304.

PMID: 16037208

Gutteridge A. & Thornton J. M. (2005)

Understanding nature's catalytic toolkit.

Trends Biochemical Science 30(11): 622-629.

PMID: 16214343

Gutteridge A. & Thornton J. M. (2005)

Conformational Changes Observed in Enzyme Crystal Structures Upon Substrate Binding.

Journal of Molecular Biology 346: 21. 28.

PMID: 15663924

Holliday G. L., Bartlett G. J., Almonacid D. E., O’Boyle N. M., Murray-Rust P., Thornton J. M. & Mitchell J. B. (2005)

MACiE: a database of enzyme reaction mechanisms. Bioinformatics.

Bioinformatics 2005 Dec 1;21(23): 4315-4316. [Epub 2005 Sep 27]

PMID: 16188925

Landau M., Mayrose I., Rosenberg Y., Glaser F., Martz E., Pupko T., Ben-Tal N. (2005)

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.

Nucleic Acids Research 33: W299-W302.

PMID: 15980475

Laskowski R. A. (2005)

Determining function from structure.

In Structural Genomics and High Throughput Structural. Biologyeds. Sundstrm M Norin M & Edwards A CRC Press Baton Rouge pp. 163-184.

Laskowski R. A., Chistyakov V. V. & Thornton J. M. (2005)

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

Nucleic Acids Research 33: D266-D268.

PMID: 15608193

Laskowski R. A., Watson J. D. & Thornton J. M. (2005)

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

Nucleic Acids Research 33: W89-W93.

PMID: 15980588

Laskowski R. A., Watson J. D. & Thornton J. M. (2005)

Protein function prediction using local 3D templates.

Journal of Molecular Biology 351: 614-626.

PMID: 16019027

Morris R. J., Kahraman A., Thornton J. M. (2005)

Binding pocket shape analysis for protein function prediction.

Acta Crystallographica Section D: Biological Crystallography 61: C156-C157.

Morris R. J., Kahraman A., Funkhouser R., Najmanovich R., Stockwell G., Glaser F., Laskowski R. & Thornton J. M. (2005)

Binding pocket shape analysis for protein function prediction. Quantitative Biology.

Shape Analysis and Wavelets 91-94 Edited by S. Barber P. D. Baxter K. V. Mardia R. E. Wells. Leeds. ISBN 0 85316 243 3.

Morris R. J., Najmanovich R. J., Kahraman A. & Thornton J. M. (2005)

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

Bioinformatics 21: 2347-2355.

PMID: 15728116

Najmanovich R. F., Torrance J. W. & Thornton J. M. (2005)

Prediction of Protein Function from Structure: Insights from Methods for the Detection of Local Structural Similarities .

BioTechniques 38(6): 847-851.

PMID: 1601854

Nimrod G., Glaser F., Steinberg D., Ben-Ta N., Pupko T. (2005)

Related Articles Links In silico identification of functional regions in proteins.

Bioinformatics 21 Suppl 1: i328-i337. [PubMed - in process]

PMID: 15961475

Nobeli I., Spriggs R. V., George R. A. & Thornton J. M. (2005)

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

Journal of Molecular Biology 347: 415-436.

PMID: 15740750

Orengo, C.A., Thornton J.M. (2005)

Protein Families and Their Evolution - a Structural Perspective.

Annual Review of Biochemistry 74: 867-900.

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., Diboun I., Addou S., Lise S., Johnston C., Sillero A., Thornton J. and Orengo C. (2005)

The Cath Domain Structure Database and Related Resources Gene3d and Dhs Provide Comprehensive Domain Family Information for Genome Analysis.

Nucleic Acids Research 33 (2005): D247-D51.

Pellegrini-Calace M. & Thornton J. M. (2005)

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

Nucleic Acids Research 33: 2129-2240.

PMID: 15831786

Ponstingl H., Kabir T., Gorse D. & Thornton J. M. (2005)

Morphological aspects of oligomeric protein structures.

Progress in Biophysics and Molecular Biology 89: 9-35.

PMID: 15831786

Ranea J. A. G., Grant A., Thornton J. M. & Orengo C. A. (2005)

Microeconomic principles explain an optimal genome size in bacteria.

Trends in Genetics 21: 21-25.

PMID: 15680509

Savchenko A., Krogan N., Cort J. R . Evdokimova E., Lew J. M., Yee A. A., Sanchez-Pulido L., Andrade M. A., Bochkarev A., Watson J. D., Kennedy M. A., Greenblatt J Hughes T., Arrowsmith C. H., Rommens J. M., Edwards A. M. (2005)

The Shwachman-Bodian-diamond syndrome protein family is involved in RNA metabolism.

Journal of Biological Chemistry 13;280(19): 19213-19220.

PMID: 15701634

Shanahan H. P. & Thornton J. M. (2005)

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

Biopolymers. 78(6): 318-328.

PMID: 15898105

Thornton J. M. & Orengo C. (2005)

“Protein Families and their evolution – A structural perspective”.

Annual Review of Biochemistry 74: 867-900.

PMID: 15954844

Todd A. E., Marsden R. L., Thornton J. M. & Orengo C. A. (2005)

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

Journal of Molecular Biology 348: 1235-1260.

PMID: 15854658

Torrance J. W. Bartlett G. J., Porter C. T. & Thornton J. M. (2005)

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

Journal of Molecular Biology 347: 565-581.

PMID: 15755451

Watson J. D., Laskowski R. A., Thornton J. M. (2005)

Predicting protein function from sequence and structural data.

Current Opinions in Structural Biology 15: 275-284.

PMID: 15755451

Watson J. D., Laskowski R. A., Thornton J. M. (2005)

Predicting protein function from sequence and structural data.

Current Opinions in Structural Biology 15: 275-284.

PMID: 15755451

Wertheim B., Kraaijeveld A. R., Schuster E., Blanc E., Hopkins M., Pletcher S. D., Strand M. R., Partridge L Godfray HC (2005)

Genome-wide gene expression in response to parasitoid attack in Drosophila

Genome Biology 2005; 6(11): R94.

PMID: 15755451

Top

2004

Auwerx J., Avner P., Baldock R., Ballabio A., Balling R., Barbacid M., Berns A., Bradley A., Brown S., Carmeliet P., Chambon P., Cox R., Davidson D., Davies K., Duboule D., Forejt J., Granucci F., Hastie N., de Angelis M. H., Jackson I., Kioussis D., Kollias G., Lathrop M., Lendahl U., Malumbres M., von Melchner H., Muller W., Partanen J., Ricciardi-Castagnoli P., Rigby P., Rosen B., Rosenthal N., Skarnes B., Stewart A. F., Thornton J., Tocchini-Valentini G., Wagner E., Wahli W. and Wurst W. (2004)

The European Dimension for the Mouse Genome Mutagenesis Program.

Nature Genetics 36, no. 9: 925-27.

Barker, J., and J. Thornton (2004)

Software Engineering Challenges in Bioinformatics.

In Icse 2004: 26th International Conference on Software Engineering, Proceedings, 12-15. Los Alamitos: Ieee Computer Soc.

Berezin C., Glaser F., Rosenberg J., Paz I., Pupko T., Fariselli P., Casadio R., & Ben-Tal N. (2004)

ConSeq: the identification of functionally and structurally important residues in protein sequences.

Bioinformatics 22;20(8): 1322-1324.

PMID: 14871869

Bray J. E., Marskden R. L., Rison S. C., Savchenko A., Edwards A. M., Thornton J. M. & Orengo C. A. (2004)

A practical and robust sequence search strategy for structural genomics target selection.

Bioinformatics 20(14): 2288-2295.

PMID: 15201178

Cohen S. X., Morris R. J., Fernandez F. J., Ben Jelloul M., Kakaris M., Parthasarathy V., Lamzin V. S., Kleywegt G. J. and Perrakis A. (2004)

Towards Complete Validated Models in the Next Generation of Arp/Warp.

Acta Crystallographica Section D-Biological Crystallography 60: 2222-29.

Eyre T. A., Partridge L. & Thornton J. M. (2004)

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

Protein Engineering Design & Selection 17(8): 613-624.

PMID: 15388845.

George R. A., Spriggs R. V., Thornton J. M. Al-Lazikani B. & Swindells M. B. (2004)

SCOPEC: a database of protein catalytic domains.

Bioinformatics 20: I130-I136.

PMID: 15262791

Gutteridge A Thornton J. (2004)

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

FEBS Letters 2004 Jun 1;567(1): 67-73. Review.

PMID: 15165895

Jones S. & Thornton J. M. (2004)

Searching for functional sites in protein structures.

Current Opinions in Chemical Biology 8(1): 3-8.

PMID: 15036149.

Macchiarulo A., Nobeli I., & Thornton J. M. (2004)

Ligand selectivity and competition between enzymes in silico.

Nature Biotechnology 22: 1039-45.

PMID: 15286657

McElwee J. J., Schuster E., Blanc E Thomas J. H., Gems D. (2004)

Shared transcriptional signature in Caenorhabditis elegans Dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance.

Journal of Biological Chemistry 279(43): 44533-44543

PMID: 15308663

Melamed D., Mark-Danieli M., Kenan-Eichler M., Kraus O., Castiel A., Laham N., Pupko T., Glaser F., Ben-Tal N., Bacharach E. (2004)

The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release.

Journal of Virology 78(18): 9675-9688.

Murray K. B., Taylor W. R. & Thornton J. M. (2004)

Toward the detection and validation of repeats in protein structure.

Proteins 57: 365-380.

PMID: 15340924

Nobeli I. & Thornton J. M. (2004)

The Metabolome.

In 'The Encyclopaedia of Computational Chemistry'. von Ragué Schleyer P. (Editor-in-Chief) Jon Wiley & Sons UK.

ISBN: 0-471-96588-X

Nobeli, I., and J. Thornton (2004)

The Proteome and the Metabolome - a Structural Perspective..

In Peptide Revolution: Genomics, Proteomics & Therapeutics, edited by M. Chorev and T. K. Sawyer, 526-33. Washington: Amer Chemical Soc, 2004.

Porter C. T., Bartlett G. J., Thornton J. M. (2004)

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

Nucleic Acids Research 32: D129-D133.

PMID: 14681376

Ranea J. A Buchan D. W., Thornton J. M. & Orengo C. A. (2004)

Evolution of protein superfamilies and bacterial genome size.

Journal of Molecular Biology 336: 871-887.

PMID: 15095866

Sanishvili R., Wu R., Kim D. E., Watson J. D., Collart F., Joachimiak A. (2004)

Crystal structure of Bacillus subtilis YckF: structural and functional evolution.

Journal of Structural Biology 2004 148(1): 98-109.

PMID: 15363790

Savchenko A., Skarina T., Evdokimova E., Watson J. D., Laskowsk i R., Arrowsmith C. H., Edwards A. M., Joachimiak A., Zhang R. G., (2004)

X-ray crystal structure of CutA from Thermotoga maritima at 1. 4 A resolution.

Proteins 54(1): 162-165.

PMID: 14705033

Shanahan H. P. & Thornton J. M. . (2004)

An examination of the conservation of surface patch polarity for proteins.

Bioinformatics 20(14): 2197-2204.

PMID:15073014

Shanahan H. P., Garcia M. A., Jones S., Thornton J. M. (2004)

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

Nucl. Acid. Rev. 32(16): 4732-4741.

PMID: 15356290

Vogel C., Berzuini C., Bashton M., Gough J., Teichmann S. A. (2004)

Supra-domains: evolutionary units larger than single protein domains.

Journal of Molecular Biology 336: 809-823.

PMID: 15095989

Vogel C., Bashton M., Kerrison N. D., Chothia C., Teichmann S. A. (2004)

Structure function and evolution of multidomain proteins.

Current Opinions in Structural Biology 14: 208-216.

PMID: 15093836

Top

2003

Barker J. A., Thornton J. M. (2003)

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

Bioinformatics 2003 Sep 1;19(13): 1644-1649.

PMID: 12967960

Bartlett G. J., Borkakoti N., Thornton J. M. (2003)

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

Journal of Molecular Biology 2003 Aug 22;331(4): 829-860.

PMID: 12909013

Bartlett G. J., Todd A. E., Thornton J. M. (2003)

Inferring protein function from structure.

Methods in Biochemical Analysis 2003;44: 387-407.

PMID: 12647396

Buchan D. W., Rison S. C., Bray J. E., Lee D., Pearl F., Thornton J. M., Orengo C. A. (2003)

Gene3D: structural assignments for the biologist and bioinformaticist alike.

Nucleic Acids Research 2003 Jan 1;31(1): 469-473.

PMID: 12520054

Dawe J. H., Porter C. T., Thornton J. M., Tabor A. B. (2003)

A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.

Proteins 2003 Aug 15;52(3): 427-435.

PMID: 12866053

Gerstein M., Thornton J. M. (2003)

Sequences and topology.

Current Opinions in Structural Biology 2003 Jun;13(3): 341-343.

PMID: 12831885

Gutteridge A., Bartlett G. J., Thornton J. M. (2003)

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

Journal of Molecular Biology 2003 Jul 18;330(4): 719-734.

PMID: 12850142

Harrison A., Pearl F., Sillitoe I., Slidel T., Mott R., Thornton J. and Orengo C. (2003)

Recognizing the Fold of a Protein Structure.

Bioinformatics 19, no. 14: 1748-59.

Jones S. and Thornton J. M. (2003)

Protein - DNA interactions: the story so far and a new method for prediction.

Comparative and Functional Genomics 4: 428-431.

Jones S., Barker J. A., Nobeli I., Thornton J. M. (2003)

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

Nucleic Acids Research 2003 Jun 1;31(11): 2811-2823.

PMID: 12771208

Jones S., Shanahan H. P., Berman H. M. and Thornton J. M. (2003)

Using Electrostatic Potentials to Predict DNA-Binding Sites on DNA-Binding Proteins.

Nucleic Acids Research 31, no. 24 (2003): 7189-98.

Laskowski R. A. (2003)

Structural quality assurance.

Methods in Biochemical Analysis 2003;44: 273-303.

PMID: 12463415

Laskowski R. A., Watson J. D., Thornton J. M. (2003)

From protein structure to biochemical function.

Journal of Structural and Functional Genomics 2003;4(2-3): 167-177.

Lebedev A. A., Tickle I. J., Laskowski R. A., Moss D. S. (2003)

Estimation of weights and validation: a marginal likelihood approach.

Acta Crystallographica Section D: Biological Crystallography 2003 Sep;59(Pt 9): 1557-1566.

PMID: 12925785

Nobeli I., Ponstingl, Krissinel E. B. and Thornton J. M. (2003)

A Structure-Based Anatomy of the E-Coli Metabolome.

Journal of Molecular Biology 334, no. 4 (2003): 697-719.

Nooren I. M., Thornton J. M. (2003)

Diversity of protein-protein interactions.

EMBO Journal 2003 Jul 15;22(14): 3486-3492.

PMID: 12853464

Nooren I. M., Thornton J. M. (2003)

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

Journal of Molecular Biology 2003 Jan 31;325(5): 991-1018.

PMID: 12527304

Orengo C. A., Pearl F. M., Thornton J. M. (2003)

The CATH domain structure database.

Methods in Biochemical Analysis 2003;44: 249-271.

PMID: 12647390

Pearl F. M. G., Bennett C. F., Bray J. E., Harrison A. P., Martin N., Shepherd A., Sillitoe I., Thornton J. and Orengo C. A. (2003)

The Cath Database: An Extended Protein Family Resource for Structural and Functional Genomics.

." Nucleic Acids Research 31, no. 1 (2003): 452-55.

Ponstingl H., Kabir T. & Thornton J. M. (2003)

Automatic Inference of Protein Quaternary Structure from Crystals.

Journal of Applied Crystallography 36: 1116-1122.

Ponstingl H. & Thornton T. M. (2003)

Proteomics: The protein complement of the genome.

The Biochemist 25: 7-9.

www. biochemist. org

Sanishvili R., Yakunin A. F., Laskowski R. A., Skarina T., Evdokimova E., Doherty-Kirby A., Lajoie G. A., Thornton J. M., Arrowsmith C. H., Savchenko A., Joachimiak A., Edwards A. M. (2003)

Integrating structure bioinformatics and enzymology to discover function: BioH a new carboxylesterase from Escherichia coli.

Journal of Biological Chemistry 2003 Jul 11;278(28): 26039-26045.

PMID: 12732651

Shepherd A. J., Gorse D., Thornton J. M. (2003)

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

Proteins 2003 Feb 1;50(2): 290-302.

PMID: 12486723

Simeonidis E., Rison S. C., Thornton J. M., Bogle I. D., Papageorgiou L. G. (2003)

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

Metabolic Engineering 2003 Jul;5(3): 211-219.

PMID: 12948755

Steward R. E., MacArthur M. W., Laskowski R. A., Thornton J. M. (2003)

Molecular basis of inherited diseases: a structural perspective.

Trends in Genetics 2003 Sep;19(9): 505-513.

PMID: 12957544

Thornton J. M., and Nobeli I. (2003)

The Proteome and the Metabolome.

Biopolymers 71, no. 3 (2003): 281.

Watson J. D., Todd A. E., Bray J., Laskowski R. A., Edwards A., Joachimiak A., Orengo C. A., Thornton J. M. (2003)

Target selection and determination of function in structural genomics.

IUBMB Life 2003 Apr-May;55(4-5): 249-255.

PMID: 12880206

Wu R. Y., Zhang R. G., Zagnitko O., Dementieva I., Maltzev N., Watson J. D., Laskowski R., Gornicki P. and Joachimiak A. (2003)

Crystal Structure of Enterococcus Faecalis Slya-Like Transcriptional Factor.

Journal of Biological Chemistry 278, no. 22 (2003): 20240-44.

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2002

Laskowski R. A., Chan A. W. (2002)

Bioinformatics and protein design.

Current Pharmaceutical Biotechnology 2002 Dec;3(4): 317-327.

PMID: 12463415

Bartlett G. J., Porter C. T., Borkakoti N., Thornton J. M. (2002)

Analysis of catalytic residues in enzyme active sites.

Journal of Molecular Biology 2002 Nov 15;324(1): 105-121.

PMID: 12421562

Harrison A., Pearl F., Mott R., Thornton J. M. & Orengo C. (2002)

Quantifying the Similarities within Fold Space

Journal of Molecular Biology 2002 Nov 8;323(5): 909-926.

PMID: 12417203

Todd A. E., Orengo C. A., Thornton J. M. (2002)

Sequence and structural differences between enzyme and nonenzyme homologs.

Structure (Camb) 2002 Oct;10(10): 1435-1451.

PMID: 12377129

Nagano N., Orengo C. A., Thornton J. M. (2002)

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

Journal of Molecular Biology 2002 Aug 30;321(5): 741-765. Review.

PMID: 12206759

de la Cruz X., Hutchinson E. G., Shepherd A., Thornton J. M. (2002)

Toward predicting protein topology: an approach to identifying beta hairpins.

The Proceedings of the National Academy of Sciences USA 2002 Aug 20;99(17): 11157-11162.

PMID: 12177429

Steward RE Thornton JM. (2002)

Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.

Proteins 2002 Aug 1;48(2): 178-191.

PMID: 12112687

Todd A. E., Orengo C. A. and Thornton J. M. (2002)

Plasticity of enzyme active sites.

Trends Biochemical Science 2002 Aug;27(8): 419-426.

PMID: 12151227

Kim Y., Skarina T., Beasley S., Laskowski R., Arrowsmith C., Joachimiak A., Edwards A. and Savchenko A. (2002)

Crystal structure of Escherichia coli EC1530 a glyoxylate induced protein YgbM.

Proteins 2002 Aug 1;48(2): 427-430.

PMID: 12112708

Luscombe N. M. and Thornton J. M. (2002)

Protein-DNA Interactions: Amino Acid Conservation and the Effects of Mutations on Binding Specificity.

Journal of Molecular Biology 2002 Jul 26;320(5): 991-1009.

PMID: 12126620

Rison S. C. and Thornton J. M. (2002)

Pathway evolution structurally speaking.

Current Opinions in Structural Biology 2002 Jun;12(3): 374-382.

PMID: 12127458

Fogh R., Ionides J., Ulrich E., Boucher W., Vranken W., Linge JP., Habeck M., Rieping W., Bhat T. N., Westbrook J., Henrick K., Gilliland G., Berman H., Thornton J., Nilges M., Markley J. and Laue E. (2002)

The CCPN project: an interim report on a data model for the NMR community.

Nature Structural biology 2002 Jun;9(6): 416-418.

PMID: 12032555

Zhang R. G., Kim Y., Skarina T., Beasley S., Laskowski R., Arrowsmith C., Edwards A., Joachimiak A. and Savchenko A. (2002)

Crystal structure of Thermotoga maritima 0065 a member of the IclR transcriptional factor family.

Journal of Biological Chemistry 2002 May 24;277(21): 19183-19190.

PMID: 11877432

Alba M. M., Laskowski R. A. and Hancock J. M. (2002)

Detecting cryptically simple protein sequences using the SIMPLE algorithm.

Bioinformatics 2002 May;18(5): 672-678.

PMID: 12050063

Rison S. C., Teichmann S. A., Thornton J. M. (2002)

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

Journal of Molecular Biology 2002 May 3;318(3): 911-932.

PMID: 12054833

Buchan D. W., Shepherd A. J., Lee D., Pearl F. M., Rison S. C., Thornton J. M. and Orengo C. A. (2002)

Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database.

Genome Research 2002 Mar;12(3): 503-514.

PMID: 11875040

Murray K. B., Gorse D., Thornton J. M. (2002)

Wavelet transforms for the characterization and detection of repeating motifs.

Journal of Molecular Biology 2002 Feb 15;316(2): 341-363.

PMID: 11851343

Martin A. C., Facchiano A. M., Cuff A. L., Hernandez-Boussard T., Olivier M., Hainaut P. and Thornton J. M. (2002)

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

Human Mutations 2002 Feb;19(2): 149-164.

PMID: 11793474

Orengo C. A., Bray J. E., Buchan D. W., Harrison A., Lee D., Pearl F. M., Sillitoe I., Todd A. E. and Thornton J. M. (2002)

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

Proteomics 2002 Jan;2(1): 11-21. Review.

PMID: 11788987

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2001

Teichmann S. A., Rison S. C., Thornton J. M., Riley M., Gough J and Chothia C. (2001)

Small-molecule metabolism: an enzyme mosaic.

Trends in Biotechnology 2001 Dec;19(12): 482-486.

PMID: 11711174

Nobeli I., Laskowski R. A., Valdar W. S. and Thornton J. M. (2001)

On the molecular discrimination between adenine and guanine by proteins.

Nucleic Acids Research 2001 Nov 1;29(21): 4294-4309.

PMID: 11691917

Nagano N., Porter C T and Thornton J. M. (2001)

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

Protein Engineering 2001 Nov;14(11): 845-855.

PMID: 11742103

Osipiuk J., Górnicki P., Maj L., Dementieva I., Laskowski R., and Joachimiak A. (2001)

Streptococcus pneumonia YlxR at 1. 35Å shows a putative new fold.

Acta Crystallographica Section D: Biological Crystallography 57: 1747-1751.

PMID: 11679764

Valdar W. S. and Thornton J. M. (2001)

Conservation helps to identify biologically relevant crystal contacts.

Journal of Molecular Biology 2001 Oct 19;313(2): 399-416.

PMID: 11800565

Teichmann S. A., Rison S. C., Thornton J. M., Riley M., Gough J. and Chothia C. (2001)

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

Journal of Molecular Biology 2001 Aug 24;311(4): 693-708.

PMID: 11518524

Luscombe N. M., Laskowski R. A. and Thornton J. M. (2001)

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

Nucleic Acids Research 2001 Jul 1;29(13): 2860-2874.

PMID: 11433033

Thornton J. M. (2001)

From genome to function.

Science 2001 Jun 15;292(5524): 2095-2097. Review. No abstract available.

PMID: 11408660

Todd A. E., Orengo C. A. and Thornton J. M. (2001)

Evolution of function in protein superfamilies from a structural perspective.

Journal of Molecular Biology 2001 Apr 6;307(4): 1113-1143.

PMID: 11286560

Jones S., Daley D. T., Luscombe N. M., Berman H. M. and Thornton J. M. (2001)

Protein-RNA interactions: a structural analysis.

Nucleic Acids Research 2001 Feb 15;29(4): 943-954.

PMID: 11160927

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. and Orengo C. A. (2001)

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

Nucleic Acids Research 2001 Jan 1;29(1): 223-227.

PMID: 11125098

Thornton J. M. (2001)

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

Protein Science 2001 Jan;10(1): 3-11.

PMID: 11266588

Laskowski R. A. (2001)

PDBsum: summaries and analyses of PDB structures.

Nucleic Acids Research 2001 Jan 1;29(1): 221-222.

PMID: 11125097

Valdar W. S. and Thornton J. M. (2001)

Protein-protein interfaces: analysis of amino acid conservation in homodimers.

Proteins 2001 Jan 1;42(1): 108-124.

PMID: 11093265

Laskowski R. A., MacArthur M. W. and Thornton J. M. (2001)

PROCHECK: validation of protein structure coordinates International Tables of Crystallography.

Volume F. Crystallography of Biological Macromolecules eds. Rossmann M G & Arnold E Dordrecht Kluwer Academic Publishers The Netherlands pp. 722-725.

Nobeli I., Mitchell J. B., Alex A. & Thornton J. M. (2001)

Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes.

Journal of Computational Chemistry 22: 673-688.

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1991-2000

Thornton Group Publications from the years 1991-2000 can be found here.

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Contact

We would like to encourage laboratories wishing to discuss any collaborations to contact us. For information comments and/or suggestions please contact us.

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