Publications

Publications

2019

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Methods in molecular biology (Clifton, N.J.) Volume 1851 (2019) p.263-275 DOI: 10.1007/978-1-4939-8736-8_14

2018

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Using the drug-protein interactome to identify anti-ageing compounds for humans
Fuentealba Valenzuela M, Donertas HM, Williams R, Labbadia J, Thornton J, Partridge L. Preprint DOI: 10.1101/438234
Transform-MinER: transforming molecules in enzyme reactions.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Bioinformatics (Oxford, England) Volume 34 (2018) p.3597-3599 DOI: 10.1093/bioinformatics/bty394
Gene expression-based drug repurposing to target aging.
Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM. Aging cell Volume 17 (2018) p.e12819 DOI: 10.1111/acel.12819
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.
Tyzack JD, Fernando L, Ribeiro AJM, Borkakoti N, Thornton JM. Structure (London, England : 1993) Volume 26 (2018) p.565-571.e3 DOI: 10.1016/j.str.2018.02.009
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Gene Expression-Based Drug Repurposing to Target Ageing
Donertas HM, Fuentealba Valenzuela M, Partridge L, Thornton J. Preprint DOI: 10.1101/253344
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Mutation accumulation differentially impacts ageing in mammalian tissues
Turan ZG, Parvizi P, Donertas HM, Tung J, Khaitovich P, Somel M. Preprint DOI: 10.1101/247700
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Nucleic acids research Volume 46 (2018) p.D618-D623 DOI: 10.1093/nar/gkx1012

2017

Editorial overview: Catalysis and regulation.
Thornton J, Orengo C. Current opinion in structural biology Volume 47 (2017) p.vi-viii DOI: 10.1016/j.sbi.2017.11.005
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Variation and Functional Impact of Neanderthal Ancestry in Western Asia.
Taskent RO, Alioglu ND, Fer E, Melike Donertas H, Somel M, Gokcumen O. Genome biology and evolution Volume 9 (2017) p.3516-3524 DOI: 10.1093/gbe/evx216
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5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction
Raiber E, Portella G, Martinez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Dawson M, Reik W, Balasubramanian S. Preprint DOI: 10.1101/224444
To what extent do structural changes in catalytic metal sites affect enzyme function?
Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. Journal of inorganic biochemistry Volume 179 (2018) p.40-53 DOI: 10.1016/j.jinorgbio.2017.11.002
Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.
Kılınç GM, Koptekin D, Atakuman Ç, Sümer AP, Dönertaş HM, Yaka R, Bilgin CC, Büyükkarakaya AM, Baird D, Altınışık E, Flegontov P, Götherström A, Togan İ, Somel M. Proceedings. Biological sciences Volume 284 (2017) DOI: 10.1098/rspb.2017.2064
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. Nucleic acids research Volume 45 (2017) p.11559-11569 DOI: 10.1093/nar/gkx814
PDBsum: Structural summaries of PDB entries.
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. Protein Science : A Publication of the Protein Society Volume 27 (2018) p.129-134 DOI: 10.1002/pro.3289
Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.
Bolukbasi E, Khericha M, Regan JC, Ivanov DK, Adcott J, Dyson MC, Nespital T, Thornton JM, Alic N, Partridge L. Cell reports Volume 21 (2017) p.641-653 DOI: 10.1016/j.celrep.2017.09.042
Understanding enzyme function evolution from a computational perspective.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Current opinion in structural biology Volume 47 (2017) p.131-139 DOI: 10.1016/j.sbi.2017.08.003
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Scientific reports Volume 7 (2017) p.5894 DOI: 10.1038/s41598-017-05927-4
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.
Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, DDD Study, Wright CF. Molecular genetics & genomic medicine Volume 5 (2017) p.495-507 DOI: 10.1002/mgg3.304
Drug repurposing for aging research using model organisms.
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Aging cell Volume 16 (2017) p.1006-1015 DOI: 10.1111/acel.12626
Common sequence variants affect molecular function more than rare variants?
Mahlich Y, Reeb J, Hecht M, Schelling M, De Beer TAP, Bromberg Y, Rost B. Scientific reports Volume 7 (2017) p.1608 DOI: 10.1038/s41598-017-01054-2
Anna Tramontano 1957-2017.
Thornton JM, Valencia A, Schwede T. Nature structural & molecular biology Volume 24 (2017) p.431-432 DOI: 10.1038/nsmb.3410
Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.
Kerr F, Sofola-Adesakin O, Ivanov DK, Gatliff J, Gomez Perez-Nievas B, Bertrand HC, Martinez P, Callard R, Snoeren I, Cochemé HM, Adcott J, Khericha M, Castillo-Quan JI, Wells G, Noble W, Thornton J, Partridge L. PLoS genetics Volume 13 (2017) p.e1006593 DOI: 10.1371/journal.pgen.1006593
New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.
Cern A, Marcus D, Tropsha A, Barenholz Y, Goldblum A. Journal of controlled release : official journal of the Controlled Release Society Volume 252 (2017) p.18-27 DOI: 10.1016/j.jconrel.2017.02.015
Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.
Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF. Human molecular genetics Volume 26 (2017) p.519-526 DOI: 10.1093/hmg/ddw409
The ProFunc Function Prediction Server.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1611 (2017) p.75-95 DOI: 10.1007/978-1-4939-7015-5_7

2016

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Drug repurposing for ageing research using model organisms
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Preprint DOI: 10.1101/095380
Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.
Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA. Journal of molecular biology Volume 428 (2016) p.3131-3146 DOI: 10.1016/j.jmb.2016.07.003
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
Jakubec D, Laskowski RA, Vondrasek J. PloS one Volume 11 (2016) p.e0158704 DOI: 10.1371/journal.pone.0158704
Rising levels of atmospheric oxygen and evolution of Nrf2.
Gacesa R, Dunlap WC, Barlow DJ, Laskowski RA, Long PF. Scientific reports Volume 6 (2016) p.27740 DOI: 10.1038/srep27740
BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.
Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS. Nucleic acids research Volume 44 (2016) p.W416-23 DOI: 10.1093/nar/gkw368
Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis.
Castillo-Quan JI, Li L, Kinghorn KJ, Ivanov DK, Tain LS, Slack C, Kerr F, Nespital T, Thornton J, Hardy J, Bjedov I, Partridge L. Cell reports Volume 15 (2016) p.638-650 DOI: 10.1016/j.celrep.2016.03.041
Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Bioinformatics (Oxford, England) Volume 32 (2016) p.2065-2066 DOI: 10.1093/bioinformatics/btw096
Exploring the chemistry and evolution of the isomerases.
Martínez Cuesta S, Rahman SA, Thornton JM. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.1796-1801 DOI: 10.1073/pnas.1509494113
Characterising Complex Enzyme Reaction Data.
Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. PloS one Volume 11 (2016) p.e0147952 DOI: 10.1371/journal.pone.0147952
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.
Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study, Wright CF. Human molecular genetics Volume 25 (2016) p.927-935 DOI: 10.1093/hmg/ddv625
Protein Structure Databases.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.31-53 DOI: 10.1007/978-1-4939-3572-7_2

2015

Synthesis of empty african horse sickness virus particles.
Maree S, Maree FF, Putterill JF, de Beer TAP, Huismans H, Theron J. Virus research Volume 213 (2016) p.184-194 DOI: 10.1016/j.virusres.2015.12.006
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.
Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA. Journal of molecular biology Volume 428 (2016) p.253-267 DOI: 10.1016/j.jmb.2015.11.010
Proteins: interaction at a distance.
Laskowski RA, Thornton JM. IUCrJ Volume 2 (2015) p.609-610 DOI: 10.1107/S2052252515020217
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.
Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N. PLoS computational biology Volume 11 (2015) p.e1004546 DOI: 10.1371/journal.pcbi.1004546
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Characterising Complex Enzyme Reaction Data
Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. Preprint DOI: 10.1101/028142
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The new science of ageing.
Partridge L, Thornton J, Bates G. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 370 (2015) DOI: 10.1098/rstb.2015.0249
SurvCurv database and online survival analysis platform update.
Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM. Bioinformatics (Oxford, England) Volume 31 (2015) p.3878-3880 DOI: 10.1093/bioinformatics/btv463
Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.
Hostaš J, Jakubec D, Laskowski RA, Gnanasekaran R, Řezáč J, Vondrášek J, Hobza P. Journal of chemical theory and computation Volume 11 (2015) p.4086-4092 DOI: 10.1021/acs.jctc.5b00398
The Classification and Evolution of Enzyme Function.
Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM. Biophysical journal Volume 109 (2015) p.1082-1086 DOI: 10.1016/j.bpj.2015.04.020
Longevity GWAS Using the Drosophila Genetic Reference Panel.
Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM. The journals of gerontology. Series A, Biological sciences and medical sciences Volume 70 (2015) p.1470-1478 DOI: 10.1093/gerona/glv047
BetaCavityWeb: a webserver for molecular voids and channels.
Kim JK, Cho Y, Lee M, Laskowski RA, Ryu SE, Sugihara K, Kim DS. Nucleic acids research Volume 43 (2015) p.W413-8 DOI: 10.1093/nar/gkv360
Reply to '"Mycobacterium indicus pranii" is a strain of Mycobacterium intracellulare': "M. indicus pranii" is a distinct strain, not derived from M. intracellulare, and is an organism at an evolutionary transition point between a fast grower and slow grower.
Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE. mBio Volume 6 (2015) DOI: 10.1128/mBio.00352-15
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Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.
Jakubec D, Hostas J, Laskowski RA, Hobza P, Vondrásek J. Journal of chemical theory and computation Volume 11 (2015) p.1939-1948 DOI: 10.1021/ct501168n
Insight into neutral and disease-associated human genetic variants through interpretable predictors.
van den Berg BA, Reinders MJ, de Ridder D, de Beer TA. PloS one Volume 10 (2015) p.e0120729 DOI: 10.1371/journal.pone.0120729
Determination of common genetic variants within the non-structural proteins of foot-and-mouth disease viruses isolated in sub-Saharan Africa.
Nsamba P, de Beer TA, Chitray M, Scott K, Vosloo W, Maree FF. Veterinary microbiology Volume 177 (2015) p.106-122 DOI: 10.1016/j.vetmic.2015.03.007
What you need to know to make the most of big data in biology.
Thornton J. Lancet (London, England) Volume 385 Suppl 1 (2015) p.S5-6 DOI: 10.1016/s0140-6736(15)60321-x

2014

Anatomy of enzyme channels.
Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M. BMC bioinformatics Volume 15 (2014) p.379 DOI: 10.1186/s12859-014-0379-x
CATH: comprehensive structural and functional annotations for genome sequences.
Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. Nucleic acids research Volume 43 (2015) p.D376-81 DOI: 10.1093/nar/gku947
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Databases and data sources: EBI and ELIXIR
Crosswell LC, Thornton JM. Comprehensive Biomedical Physics Vol. 6: Bioinformatics Elsevier
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
Papatheodorou I, Petrovs R, Thornton JM. Bioinformatics (Oxford, England) Volume 30 (2014) p.2999-3003 DOI: 10.1093/bioinformatics/btu493
The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. Current opinion in structural biology Volume 26 (2014) p.121-130 DOI: 10.1016/j.sbi.2014.06.002
Exploring the biological and chemical complexity of the ligases.
Holliday GL, Rahman SA, Furnham N, Thornton JM. Journal of molecular biology Volume 426 (2014) p.2098-2111 DOI: 10.1016/j.jmb.2014.03.008
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BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
Kim JK, Cho Y, Laskowski RA, Ryu SE, Sugihara K, Kim DS. Proteins Volume 82 (2014) p.1829-1849 DOI: 10.1002/prot.24537
DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.
Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D. PLoS genetics Volume 10 (2014) p.e1004109 DOI: 10.1371/journal.pgen.1004109
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MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.
Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D. Aging Volume 6 (2014) p.98-117 DOI: 10.18632/aging.100638
EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM. Nature methods Volume 11 (2014) p.171-174 DOI: 10.1038/nmeth.2803
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The NAD Binding Domain and the Short Chain Dehydrogenase/Reductase (SDR) Superfamily
Furnham N, Holliday GL, Thornton JM. Protein Families: Relating Protein Sequence, Structure and Function Wiley, UK
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Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM. Nature methods Volume 11 (2014) p.171-174

2013

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. PLoS computational biology Volume 9 (2013) p.e1003382 DOI: 10.1371/journal.pcbi.1003382
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. Nucleic acids research Volume 42 (2014) p.D485-9 DOI: 10.1093/nar/gkt1243
The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. Nucleic acids research Volume 42 (2014) p.D18-25 DOI: 10.1093/nar/gkt1206
LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM. Acta Crystallographica Section D: Biological Crystallography Volume 69 (2013) p.2395-2402 DOI: 10.1107/S0907444913022294
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Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa.
Chitray M, de Beer TA, Vosloo W, Maree FF. Archives of virology Volume 159 (2014) p.947-961 DOI: 10.1007/s00705-013-1838-9
PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA. Nucleic acids research Volume 42 (2014) p.D292-6 DOI: 10.1093/nar/gkt940
Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Ziehm M, Piper MD, Thornton JM. Aging cell Volume 12 (2013) p.917-922 DOI: 10.1111/acel.12123
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
Ziehm M, Thornton JM. Aging cell Volume 12 (2013) p.910-916 DOI: 10.1111/acel.12121
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Correction.
Journal of the American Chemical Society Volume 135 (2013) p.10178 DOI: 10.1021/ja403136h
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Analysis of SAT type foot-and-mouth disease virus capsid proteins and the identification of putative amino acid residues affecting virus stability.
Maree FF, Blignaut B, de Beer TA, Rieder E. PloS one Volume 8 (2013) p.e61612 DOI: 10.1371/journal.pone.0061612
Elucidating human phosphatase-substrate networks.
Li X, Wilmanns M, Thornton J, Köhn M. Science signaling Volume 6 (2013) p.rs10 DOI: 10.1126/scisignal.2003203
Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM. Molecular bioSystems Volume 9 (2013) p.1756-1764 DOI: 10.1039/c3mb25485b
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Implication of a rare deletion at distal 16p11.2 in schizophrenia.
Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, Malhotra AK, Rietschel M, Nöthen MM, Degenhardt F, Priebe L, Breuer R, Strohmaier J, Ruderfer DM, Moran JL, Chambert KD, Sanders AR, Shi J, Kendler K, Riley B, O'Neill T, Walsh D, Malhotra D, Corvin A, Purcell S, Sklar P, Iwata N, Hultman CM, Sullivan PF, Sebat J, McCarthy S, Gejman PV, Levinson DF, Owen MJ, O'Donovan MC, Lencz T, Kirov G, Molecular Genetics of Schizophrenia Consortium, Wellcome Trust Case Control Consortium 2. JAMA psychiatry Volume 70 (2013) p.253-260 DOI: 10.1001/2013.jamapsychiatry.71
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Protein Data Resources
Furnham N, Garavelli JS, Thornton JM. Encyclopaedia of Biological Chemistry Academic Press (2nd Ed)
The Ramachandran plot and protein structure validation
Laskowski RA, Furnham N, Thornton JM. Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map World Scientific Publishing DOI: 10.1142/9789814449144_0005
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The Ramachandran Plot and Protein Structure Validation
Laskowski RA, Furnham N, Thornton JM. Biomolecular Forms and Functions, A Celebration of 50 years of the Ramachandran Map World Scientific Publishing

2012

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM. PloS one Volume 7 (2012) p.e50881 DOI: 10.1371/journal.pone.0050881
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New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA. Nucleic acids research Volume 41 (2013) p.D490-8 DOI: 10.1093/nar/gks1211
The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D773-80 DOI: 10.1093/nar/gks1112
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A genome-wide study shows a limited contribution of rare copy number variants to Alzheimer's disease risk.
Chapman J, Rees E, Harold D, Ivanov D, Gerrish A, Sims R, Hollingworth P, Stretton A, GERAD1 Consortium, Holmans P, Owen MJ, O'Donovan MC, Williams J, Kirov G. Human molecular genetics Volume 22 (2013) p.816-824 DOI: 10.1093/hmg/dds476
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Serotonin: from top to bottom.
Fidalgo S, Ivanov DK, Wood SH. Biogerontology Volume 14 (2013) p.21-45 DOI: 10.1007/s10522-012-9406-3
Abstracting knowledge from the Protein Data Bank.
Furnham N, Laskowski RA, Thornton JM. Biopolymers Volume 99 (2013) p.183-188 DOI: 10.1002/bip.22107
Current challenges in genome annotation through structural biology and bioinformatics.
Furnham N, de Beer TA, Thornton JM. Current opinion in structural biology Volume 22 (2012) p.594-601 DOI: 10.1016/j.sbi.2012.07.005
ELIXIR: a distributed infrastructure for European biological data.
Crosswell LC, Thornton JM. Trends in biotechnology Volume 30 (2012) p.241-242 DOI: 10.1016/j.tibtech.2012.02.002
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Cell proliferation and migration are modulated by Cdk-1-phosphorylated endothelial-monocyte activating polypeptide II.
Schwarz MA, Thornton J, Xu H, Awasthi N, Schwarz RE. PloS one Volume 7 (2012) p.e33101 DOI: 10.1371/journal.pone.0033101
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM. PLoS computational biology Volume 8 (2012) p.e1002403 DOI: 10.1371/journal.pcbi.1002403
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Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles.
Wang T, Schiffels D, Cuesta SM, Fygenson DK, Seeman NC. Journal of the American Chemical Society Volume 134 (2012) p.1606-1616 DOI: 10.1021/ja207976q
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Women in science.
Dean C, Osborn M, Oshlack A, Thornton J. Genome biology Volume 13 (2012) p.148 DOI: 10.1186/gb-2012-13-3-148
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The role of variation at AβPP, PSEN1, PSEN2, and MAPT in late onset Alzheimer's disease.
Gerrish A, Russo G, Richards A, Moskvina V, Ivanov D, Harold D, Sims R, Abraham R, Hollingworth P, Chapman J, Hamshere M, Pahwa JS, Dowzell K, Williams A, Jones N, Thomas C, Stretton A, Morgan AR, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Morgan K, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Johnston JA, Holmes C, Mann D, Smith AD, Love S, Kehoe PG, Hardy J, Mead S, Fox N, Rossor M, Collinge J, Maier W, Jessen F, Kölsch H, Heun R, Schürmann B, van den Bussche H, Heuser I, Kornhuber J, Wiltfang J, Dichgans M, Frölich L, Hampel H, Hüll M, Rujescu D, Goate AM, Kauwe JS, Cruchaga C, Nowotny P, Morris JC, Mayo K, Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Davies G, Harris SE, Starr JM, Deary IJ, Al-Chalabi A, Shaw CE, Tsolaki M, Singleton AB, Guerreiro R, Mühleisen TW, Nöthen MM, Moebus S, Jöckel KH, Klopp N, Wichmann HE, Carrasquillo MM, Pankratz VS, Younkin SG, Jones L, Holmans PA, O'Donovan MC, Owen MJ, Williams J. Journal of Alzheimer's disease : JAD Volume 28 (2012) p.377-387 DOI: 10.3233/JAD-2011-110824
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Shouldn't enantiomeric purity be included in the minimum information about a bioactive entity? Response from the MIABE group
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 RK, Murray-Rust P, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Nature reviews. Drug discovery Volume 11 (2012) p.730 DOI: 10.1038/nrd3503-c2
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Delivering ICT Infrastructure for Biomedical Research
Nyronen TH, Laitinen J, Tourunen O, Sternkopf D, Laurikainen R, Oster P, Lehtovuori PT, Miettinen TA, Simonen T, Perheentupa T, Vastrik I, Kallioniemi O, Lyall A, Thornton JM.

2011

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Celebrating structural biology.
Nature structural & molecular biology Volume 18 (2011) p.1304-1316 DOI: 10.1038/nsmb1211-1304
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De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.
Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M, Ruderfer D, Moran J, Chambert K, Toncheva D, Georgieva L, Grozeva D, Fjodorova M, Wollerton R, Rees E, Nikolov I, van de Lagemaat LN, Bayés A, Fernandez E, Olason PI, Böttcher Y, Komiyama NH, Collins MO, Choudhary J, Stefansson K, Stefansson H, Grant SG, Purcell S, Sklar P, O'Donovan MC, Owen MJ. Molecular psychiatry Volume 17 (2012) p.142-153 DOI: 10.1038/mp.2011.154
*
POPISK: T-cell reactivity prediction using support vector machines and string kernels.
Tung CW, Ziehm M, Kämper A, Kohlbacher O, Ho SY. BMC bioinformatics Volume 12 (2011) p.446 DOI: 10.1186/1471-2105-12-446
*
Structural annotation of Mycobacterium tuberculosis proteome.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R, OSDD Consortium, Brahmachari SK, Chandra N. PloS one Volume 6 (2011) p.e27044 DOI: 10.1371/journal.pone.0027044
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM. Nucleic acids research Volume 40 (2012) p.D776-82 DOI: 10.1093/nar/gkr852
LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB. Journal of chemical information and modeling Volume 51 (2011) p.2778-2786 DOI: 10.1021/ci200227u
*
De novo induction of amyloid-β deposition in vivo.
Morales R, Duran-Aniotz C, Castilla J, Estrada LD, Soto C. Molecular psychiatry Volume 17 (2012) p.1347-1353 DOI: 10.1038/mp.2011.120
*
Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.
Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP. Genome biology Volume 12 (2011) p.R90 DOI: 10.1186/gb-2011-12-9-r90
Minimum information about a bioactive entity (MIABE).
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 RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Nature reviews. Drug discovery Volume 10 (2011) p.661-669 DOI: 10.1038/nrd3503
The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.
McParland V, Varsano G, Li X, Thornton J, Baby J, Aravind A, Meyer C, Pavic K, Rios P, Köhn M. Biochemistry Volume 50 (2011) p.7579-7590 DOI: 10.1021/bi201095z
*
Predicting antigenic sites on the foot-and-mouth disease virus capsid of the South African Territories types using virus neutralization data.
Maree FF, Blignaut B, Esterhuysen JJ, de Beer TA, Theron J, O'Neill HG, Rieder E. The Journal of general virology Volume 92 (2011) p.2297-2309 DOI: 10.1099/vir.0.032839-0
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Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.
Alic N, Andrews TD, Giannakou ME, Papatheodorou I, Slack C, Hoddinott MP, Cochemé HM, Schuster EF, Thornton JM, Partridge L. Molecular systems biology Volume 7 (2011) p.502 DOI: 10.1038/msb.2011.36
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.
Holliday GL, Fischer JD, Mitchell JB, Thornton JM. The FEBS journal Volume 278 (2011) p.3835-3845 DOI: 10.1111/j.1742-4658.2011.08190.x
Protein structure databases.
Laskowski RA. Molecular biotechnology Volume 48 (2011) p.183-198 DOI: 10.1007/s12033-010-9372-4
*
1,000 structures and more from the MCSG.
Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA. BMC structural biology Volume 11 (2011) p.2 DOI: 10.1186/1472-6807-11-2
*
The new science of ageing.
Partridge L, Thornton J, Bates G. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.6-8 DOI: 10.1098/rstb.2010.0298
Computational biology for ageing.
Wieser D, Papatheodorou I, Ziehm M, Thornton JM. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 366 (2011) p.51-63 DOI: 10.1098/rstb.2010.0286

2010

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Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus.
Reeve R, Blignaut B, Esterhuysen JJ, Opperman P, Matthews L, Fry EE, de Beer TA, Theron J, Rieder E, Vosloo W, O'Neill HG, Haydon DT, Maree FF. PLoS computational biology Volume 6 (2010) p.e1001027 DOI: 10.1371/journal.pcbi.1001027
*
Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA. Nucleic acids research Volume 39 (2011) p.D420-6 DOI: 10.1093/nar/gkq1001
The structures and physicochemical properties of organic cofactors in biocatalysis.
Fischer JD, Holliday GL, Rahman SA, Thornton JM. Journal of molecular biology Volume 403 (2010) p.803-824 DOI: 10.1016/j.jmb.2010.09.018
The CoFactor database: organic cofactors in enzyme catalysis.
Fischer JD, Holliday GL, Thornton JM. Bioinformatics (Oxford, England) Volume 26 (2010) p.2496-2497 DOI: 10.1093/bioinformatics/btq442
*
DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.
Schuster E, McElwee JJ, Tullet JM, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D. Molecular systems biology Volume 6 (2010) p.399 DOI: 10.1038/msb.2010.54
*
Heme proteins--diversity in structural characteristics, function, and folding.
Smith LJ, Kahraman A, Thornton JM. Proteins Volume 78 (2010) p.2349-2368 DOI: 10.1002/prot.22747
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Mapping of amino acid residues responsible for adhesion of cell culture-adapted foot-and-mouth disease SAT type viruses.
Maree FF, Blignaut B, de Beer TA, Visser N, Rieder EA. Virus research Volume 153 (2010) p.82-91 DOI: 10.1016/j.virusres.2010.07.010
Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.
Berka K, Laskowski RA, Hobza P, Vondrášek J. Journal of chemical theory and computation Volume 6 (2010) p.2191-2203 DOI: 10.1021/ct100007y
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM. Proteins Volume 78 (2010) p.1120-1136 DOI: 10.1002/prot.22633
*
Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan AW, Laskowski RA, Selwood DL. Journal of medicinal chemistry Volume 53 (2010) p.3086-3094 DOI: 10.1021/jm901696w
*
Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.
Slack C, Werz C, Wieser D, Alic N, Foley A, Stocker H, Withers DJ, Thornton JM, Hafen E, Partridge L. PLoS genetics Volume 6 (2010) p.e1000881 DOI: 10.1371/journal.pgen.1000881
*
ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri AU, Laskowski RA. Bioinformatics Volume 26 (2010) p.1260-1261 DOI: 10.1093/bioinformatics/btq119
Domain-ligand mapping for enzymes.
Bashton M, Thornton JM. Journal of molecular recognition : JMR Volume 23 (2010) p.194-208 DOI: 10.1002/jmr.992
Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ. Nature methods Volume 7 (2010) p.S42-55 DOI: 10.1038/nmeth.1427
*
Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M. Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.4135-4140 DOI: 10.1073/pnas.0910632107
The (non)malignancy of cancerous amino acidic substitutions.
Talavera D, Taylor MS, Thornton JM. Proteins Volume 78 (2010) p.518-529 DOI: 10.1002/prot.22574
*
The malarial drug target Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PfDXR): development of a 3-D model for identification of novel, structural and functional features and for inhibitor screening.
Goble JL, Adendorff MR, de Beer TA, Stephens LL, Blatch GL. Protein and peptide letters Volume 17 (2010) p.109-120 DOI: 10.2174/092986610789909548
Protein structure databases.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 609 (2010) p.59-82 DOI: 10.1007/978-1-60327-241-4_4

2009

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Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. PLoS computational biology Volume 5 (2009) p.e1000585 DOI: 10.1371/journal.pcbi.1000585
The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J. Nucleic acids research Volume 38 (2010) p.D17-25 DOI: 10.1093/nar/gkp986
*
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJ, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AF, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C. Nature genetics Volume 41 (2009) p.1182-1190 DOI: 10.1038/ng.467
*
Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I. Journal of chemical information and modeling Volume 49 (2009) p.2272-2289 DOI: 10.1021/ci900196u
*
Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M, Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, Thomas G, Carling D, Okkenhaug K, Thornton JM, Partridge L, Gems D, Withers DJ. Science (New York, N.Y.) Volume 326 (2009) p.140-144 DOI: 10.1126/science.1177221
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PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva R, Thornton JM, Pellegrini-Calace M. Bioinformatics (Oxford, England) Volume 25 (2009) p.3183-3184 DOI: 10.1093/bioinformatics/btp545
*
Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J. Nature Volume 461 (2009) p.168-170 DOI: 10.1038/461168a
Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Journal of cheminformatics Volume 1 (2009) p.12 DOI: 10.1186/1758-2946-1-12
Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM. Nature chemical biology Volume 5 (2009) p.521-525 DOI: 10.1038/nchembio0809-521
*
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C. Structure (London, England : 1993) Volume 17 (2009) p.1051-1062 DOI: 10.1016/j.str.2009.06.015
The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ. Biochemical Society transactions Volume 37 (2009) p.723-726 DOI: 10.1042/bst0370723
*
Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria.
Joubert F, Harrison CM, Koegelenberg RJ, Odendaal CJ, de Beer TA. Malaria journal Volume 8 (2009) p.178 DOI: 10.1186/1475-2875-8-178
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace M, Maiwald T, Thornton JM. PLoS computational biology Volume 5 (2009) p.e1000440 DOI: 10.1371/journal.pcbi.1000440
Protein Evolution – Sequence, Structure and Systems
Sternberg M, Thornton J, Laskowski R. The Biochemist Biochemical Society
Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday GL, Mitchell JB, Thornton JM. Journal of molecular biology Volume 390 (2009) p.560-577 DOI: 10.1016/j.jmb.2009.05.015
*
Metal-MACiE: a database of metals involved in biological catalysis.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Bioinformatics (Oxford, England) Volume 25 (2009) p.2088-2089 DOI: 10.1093/bioinformatics/btp256
Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.
Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J. Journal of chemical theory and computation Volume 5 (2009) p.982-992 DOI: 10.1021/ct800508v
The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM. FEBS letters Volume 583 (2009) p.1692-1698 DOI: 10.1016/j.febslet.2009.03.019
*
Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Journal of molecular biology Volume 388 (2009) p.356-380 DOI: 10.1016/j.jmb.2009.02.052
WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM. Bioinformatics Volume 25 (2009) p.1192-1194 DOI: 10.1093/bioinformatics/btp116
*
Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network. Genome biology Volume 10 (2009) p.401 DOI: 10.1186/gb-2009-10-2-401
*
Protein function annotation by homology-based inference.
Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A. Genome biology Volume 10 (2009) p.207 DOI: 10.1186/gb-2009-10-2-207
Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM. Journal of the Royal Society, Interface Volume 6 (2009) p.129-147 DOI: 10.1098/rsif.2008.0341
*
Protein promiscuity and its implications for biotechnology.
Nobeli I, Favia AD, Thornton JM. Nature biotechnology Volume 27 (2009) p.157-167 DOI: 10.1038/nbt1519
New open drug activity data at EBI
Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J. Chemistry Central journal Volume 3 (2009) p.O3 DOI: 10.1186/1752-153x-3-s1-o3
Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Watson JD, Thornton JM. From Molecules to Medicines: Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism Springer Netherlands DOI: 10.1007/978-90-481-2339-1_13
Integrated Servers for Structure-Informed Function Prediction
Laskowski RA. From Protein Structure to Function with Bioinformatics Springer Netherlands DOI: 10.1007/978-1-4020-9058-5_10

2008

PDBsum new things.
Laskowski RA. Nucleic acids research Volume 37 (2009) p.D355-9 DOI: 10.1093/nar/gkn860
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The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA. Nucleic acids research Volume 37 (2009) p.D310-4 DOI: 10.1093/nar/gkn877
*
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U. Chemico-biological interactions Volume 178 (2009) p.94-98 DOI: 10.1016/j.cbi.2008.10.040
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. Bioinformatics (Oxford, England) Volume 24 (2008) p.2767-2772 DOI: 10.1093/bioinformatics/btn528
Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM. BMC evolutionary biology Volume 8 (2008) p.247 DOI: 10.1186/1471-2148-8-247
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J. Bioinformatics (Oxford, England) Volume 24 (2008) p.i105-11 DOI: 10.1093/bioinformatics/btn263
*
Metal ions in biological catalysis: from enzyme databases to general principles.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry Volume 13 (2008) p.1205-1218 DOI: 10.1007/s00775-008-0404-5
Evolution of binding sites for zinc and calcium ions playing structural roles.
Torrance JW, Macarthur MW, Thornton JM. Proteins Volume 71 (2008) p.813-830 DOI: 10.1002/prot.21741
Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM. Nature reviews. Genetics Volume 9 (2008) p.141-151 DOI: 10.1038/nrg2273
*
Methods to Characterize the Structure of Enzyme Binding Sites
Kahraman A and Thornton JM. Computational Structural Biology - Methods and Applications World Scientific Publishing

2007

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. BMC bioinformatics Volume 8 (2007) p.S1-S1
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD, Nobeli I, Glaser F, Thornton JM. Journal of molecular biology Volume 375 (2008) p.855-874 DOI: 10.1016/j.jmb.2007.10.065
*
Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
Selman C, Lingard S, Choudhury AI, Batterham RL, Claret M, Clements M, Ramadani F, Okkenhaug K, Schuster E, Blanc E, Piper MD, Al-Qassab H, Speakman JR, Carmignac D, Robinson IC, Thornton JM, Gems D, Partridge L, Withers DJ. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 22 (2008) p.807-818 DOI: 10.1096/fj.07-9261com
*
Construction, visualisation, and clustering of transcription networks from microarray expression data.
Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ. PLoS computational biology Volume 3 (2007) p.2032-2042 DOI: 10.1371/journal.pcbi.0030206
Evolution of enzymes and pathways for the biosynthesis of cofactors.
Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ. Natural product reports Volume 24 (2007) p.972-987 DOI: 10.1039/b703107f
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM. PLoS computational biology Volume 3 (2007) p.1993-2002 DOI: 10.1371/journal.pcbi.0030198
PROCOGNATE: a cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM. Nucleic acids research Volume 36 (2008) p.D618-22 DOI: 10.1093/nar/gkm611
The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. Journal of molecular biology Volume 372 (2007) p.1261-1277 DOI: 10.1016/j.jmb.2007.07.034
*
Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases.
Allali-Hassani A, Pan W, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards A, Bochkarev A, Plotnikov A, Vedadi M, Arrowsmith C. PLoS biology Volume 5 (2007)
*
Structural and chemical profiling of the human cytosolic sulfotransferases.
Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. PLoS biology Volume 5 (2007) p.e97 DOI: 10.1371/journal.pbio.0050097
Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA. Bioinformatics Volume 23 (2007) p.1824-1827 DOI: 10.1093/bioinformatics/btm085
The geometry of interactions between catalytic residues and their substrates.
Torrance JW, Holliday GL, Mitchell JB, Thornton JM. Journal of molecular biology Volume 369 (2007) p.1140-1152 DOI: 10.1016/j.jmb.2007.03.055
*
The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, 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 SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A. Proceedings of the National Academy of Sciences of the United States of America Volume 104 (2007) p.5495-5500 DOI: 10.1073/pnas.0700800104
Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Journal of molecular biology Volume 368 (2007) p.283-301 DOI: 10.1016/j.jmb.2007.01.086
Towards fully automated structure-based function prediction in structural genomics: a case study.
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM. Journal of molecular biology Volume 367 (2007) p.1511-1522 DOI: 10.1016/j.jmb.2007.01.063
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM. Bioinformatics (Oxford, England) Volume 23 (2007) p.e104-9 DOI: 10.1093/bioinformatics/btl292
*
Evolutionary conservation of regulated longevity assurance mechanisms.
McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas JH, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D. Genome biology Volume 8 (2007) p.R132 DOI: 10.1186/gb-2007-8-7-r132
Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Schuster EF, Blanc E, Partridge L, Thornton JM. Genome biology Volume 8 (2007) p.R126 DOI: 10.1186/gb-2007-8-6-r126
Correcting for sequence biases in present/absent calls.
Schuster EF, Blanc E, Partridge L, Thornton JM. Genome biology Volume 8 (2007) p.R125 DOI: 10.1186/gb-2007-8-6-r125
*
Evolving Methods for Macromolecular Crystallography
Watson J, Golovin A, Laskowski R, Henrick K, Thornton JM, Joachimiak A and Edwards A. Structural Bioinformatics: From Protein Structure to Function
*
Variation of geometrical and phsicochemical properties in protein binding pockets and their ligands
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. BMC Bioinformatics (8 edition)

2006

*
Erratum to "Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans" [Mech. Ageing Dev. 127 (5) (2006) 458-472].
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D. Mechanisms of ageing and development Volume 127 (2006) p.922-936 DOI: 10.1016/j.mad.2006.10.002
*
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. Nucleic acids research Volume 35 (2007) p.D291-7 DOI: 10.1093/nar/gkl959
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM. Nucleic acids research Volume 35 (2007) p.D515-20 DOI: 10.1093/nar/gkl774
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.
Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM. Genome biology Volume 7 (2006) p.R89 DOI: 10.1186/gb-2006-7-10-r89
*
Protein superfamily evolution and the last universal common ancestor (LUCA).
Ranea JA, Sillero A, Thornton JM, Orengo CA. Journal of molecular evolution Volume 63 (2006) p.513-525 DOI: 10.1007/s00239-005-0289-7
Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM. Journal of molecular biology Volume 364 (2006) p.836-852 DOI: 10.1016/j.jmb.2006.09.041
*
SPINE bioinformatics and data-management aspects of high-throughput structural biology.
Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K. Acta crystallographica. Section D, Biological crystallography Volume 62 (2006) p.1184-1195 DOI: 10.1107/s090744490602991x
*
Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.
Selman C, Kerrison ND, Cooray A, Piper MD, Lingard SJ, Barton RH, Schuster EF, Blanc E, Gems D, Nicholson JK, Thornton JM, Partridge L, Withers DJ. Physiological genomics Volume 27 (2006) p.187-200 DOI: 10.1152/physiolgenomics.00084.2006
*
A bioinformatician's view of the metabolome.
Nobeli I, Thornton JM. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 28 (2006) p.534-545 DOI: 10.1002/bies.20414
Integrating biological data through the genome.
Reeves GA, Thornton JM, BioSapiens Network of Excellence. Human molecular genetics Volume 15 Spec No 1 (2006) p.R81-7 DOI: 10.1093/hmg/ddl086
*
An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Whamond GS, Thornton JM. Journal of molecular biology Volume 359 (2006) p.238-247 DOI: 10.1016/j.jmb.2006.03.029
*
Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.
Zhang R, Skarina T, Evdokimova E, Edwards A, Savchenko A, Laskowski R, Cuff ME, Joachimiak A. Acta crystallographica. Section F, Structural biology and crystallization communications Volume 62 (2006) p.335-339 DOI: 10.1107/S1744309106009651
*
Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans.
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D. Mechanisms of ageing and development Volume 127 (2006) p.458-472 DOI: 10.1016/j.mad.2006.01.006
*
Introduction. Bioinformatics: from molecules to systems.
Jones DT, Sternberg MJ, Thornton JM. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 361 (2006) p.389-391 DOI: 10.1098/rstb.2005.1811
A method for localizing ligand binding pockets in protein structures.
Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM. Proteins Volume 62 (2006) p.479-488 DOI: 10.1002/prot.20769
*
Introduction. Bioinformatics: From Molecules to Systems
Jones DT, Sternberg MJE, Thornton JM. Philosophical Transactions of the Royal Society of London Series B - Biological Sciences (361 edition)

2005

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM. Journal of molecular biology Volume 356 (2006) p.928-944 DOI: 10.1016/j.jmb.2005.12.012
*
Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression.
Giannattasio S, Liu Z, Thornton J, Butow RA. The Journal of biological chemistry Volume 280 (2005) p.42528-42535 DOI: 10.1074/jbc.m509187200
Understanding nature's catalytic toolkit.
Gutteridge A, Thornton JM. Trends in biochemical sciences Volume 30 (2005) p.622-629 DOI: 10.1016/j.tibs.2005.09.006
*
MACiE: a database of enzyme reaction mechanisms.
Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. Bioinformatics (Oxford, England) Volume 21 (2005) p.4315-4316 DOI: 10.1093/bioinformatics/bti693
Morphological aspects of oligomeric protein structures.
Ponstingl H, Kabir T, Gorse D, Thornton JM. Progress in biophysics and molecular biology Volume 89 (2005) p.9-35 DOI: 10.1016/j.pbiomolbio.2004.07.010
*
Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
Shanahan HP, Thornton JM. Biopolymers Volume 78 (2005) p.318-328 DOI: 10.1002/bip.20295
Protein function prediction using local 3D templates.
Laskowski RA, Watson JD, Thornton JM. Journal of molecular biology Volume 351 (2005) p.614-626 DOI: 10.1016/j.jmb.2005.05.067
*
Effective function annotation through catalytic residue conservation.
George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB. Proceedings of the National Academy of Sciences of the United States of America Volume 102 (2005) p.12299-12304 DOI: 10.1073/pnas.0504833102
*
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
Ferrer-Costa C, Shanahan HP, Jones S, Thornton JM. Bioinformatics (Oxford, England) Volume 21 (2005) p.3679-3680 DOI: 10.1093/bioinformatics/bti575
ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM. Nucleic acids research Volume 33 (2005) p.W89-93 DOI: 10.1093/nar/gki414
Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM. Genome biology Volume 6 (2005) p.R56 DOI: 10.1186/gb-2005-6-7-r56
Prediction of protein function from structure: insights from methods for the detection of local structural similarities.
Najmanovich RJ, Torrance JW, Thornton JM. BioTechniques Volume 38 (2005) p.847, 849, 851 DOI: 10.2144/05386te01
The complement of enzymatic sets in different species.
Freilich S, Spriggs RV, George RA, Al-Lazikani B, Swindells M, Thornton JM. Journal of molecular biology Volume 349 (2005) p.745-763 DOI: 10.1016/j.jmb.2005.04.027
*
Prediction of Protein Function from Structure: Insights from Methods for the Detection of Local Structural Similarities
Najmanovich RF, Torrance JW, Thornton JM. BioTechniques Volume 38 (2005) p.847-851 DOI: 10.2144/05386te01
Predicting protein function from sequence and structural data.
Watson JD, Laskowski RA, Thornton JM. Current opinion in structural biology Volume 15 (2005) p.275-284 DOI: 10.1016/j.sbi.2005.04.003
Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.
Pellegrini-Calace M, Thornton JM. Nucleic acids research Volume 33 (2005) p.2129-2140 DOI: 10.1093/nar/gki349
*
Progress of structural genomics initiatives: an analysis of solved target structures.
Todd AE, Marsden RL, Thornton JM, Orengo CA. Journal of molecular biology Volume 348 (2005) p.1235-1260 DOI: 10.1016/j.jmb.2005.03.037
Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.
Torrance JW, Bartlett GJ, Porter CT, Thornton JM. Journal of molecular biology Volume 347 (2005) p.565-581 DOI: 10.1016/j.jmb.2005.01.044
A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.
Nobeli I, Spriggs RV, George RA, Thornton JM. Journal of molecular biology Volume 347 (2005) p.415-436 DOI: 10.1016/j.jmb.2005.01.061
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM. Bioinformatics (Oxford, England) Volume 21 (2005) p.2347-2355 DOI: 10.1093/bioinformatics/bti337
*
Binding Pocket Shape Analysis for Protein Function Prediction
Morris RJ, Kahraman A, Thornton JM. Acta crystallographica Volume D61 (2005) p.C156-C157
*
Microeconomic principles explain an optimal genome size in bacteria.
Ranea JA, Grant A, Thornton JM, Orengo CA. Trends in genetics : TIG Volume 21 (2005) p.21-25 DOI: 10.1016/j.tig.2004.11.014
*
Binding pocket shape analysis for protein function prediction
Morris RJ, Kahraman A, Funkhouser T, Najmanovich R, Stockwell G, Glaser F, Laskowski R, Thornton JM. Quantitative Biology, Shape Analysis and Wavelets
*
Protein families and their evolution-a structural perspective.
Orengo CA, Thornton JM. Annual review of biochemistry Volume 74 (2005) p.867-900 DOI: 10.1146/annurev.biochem.74.082803.133029
*
Shape-based classification of bound ligands
Funkhouser T, Glaser F, Laskowski R, Morris RJ, Najmanovich R, Stockwell G, Thornton JM. Quantitative Biology, Shape Analysis and Wavelets
*
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
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, Orengo C. Nucleic acids research Volume 33 (2005) p.D247-51 DOI: 10.1093/nar/gki024
The European Bioinformatics Institute's data resources: towards systems biology.
Brooksbank C, Cameron G, Thornton J. Nucleic acids research Volume 33 (2005) p.D46-53 DOI: 10.1093/nar/gki026
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Laskowski RA, Chistyakov VV, Thornton JM. Nucleic acids research Volume 33 (2005) p.D266-8 DOI: 10.1093/nar/gki001

2004

Conformational changes observed in enzyme crystal structures upon substrate binding.
Gutteridge A, Thornton J. Journal of molecular biology Volume 346 (2005) p.21-28 DOI: 10.1016/j.jmb.2004.11.013
Toward the detection and validation of repeats in protein structure.
Murray KB, Taylor WR, Thornton JM. Proteins Volume 57 (2004) p.365-380 DOI: 10.1002/prot.20202
Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
Shanahan HP, Garcia MA, Jones S, Thornton JM. Nucleic acids research Volume 32 (2004) p.4732-4741 DOI: 10.1093/nar/gkh803
*
The European dimension for the mouse genome mutagenesis program.
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 MH, Jackson I, Kioussis D, Kollias G, Lathrop M, Lendahl U, Malumbres M, von Melchner H, Müller W, Partanen J, Ricciardi-Castagnoli P, Rigby P, Rosen B, Rosenthal N, Skarnes B, Stewart AF, Thornton J, Tocchini-Valentini G, Wagner E, Wahli W, Wurst W. Nature genetics Volume 36 (2004) p.925-927 DOI: 10.1038/ng0904-925
*
Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
Eyre TA, Partridge L, Thornton JM. Protein engineering, design & selection : PEDS Volume 17 (2004) p.613-624 DOI: 10.1093/protein/gzh072
Ligand selectivity and competition between enzymes in silico.
Macchiarulo A, Nobeli I, Thornton JM. Nature biotechnology Volume 22 (2004) p.1039-1045 DOI: 10.1038/nbt999
*
SCOPEC: a database of protein catalytic domains.
George RA, Spriggs RV, Thornton JM, Al-Lazikani B, Swindells MB. Bioinformatics Volume 20 Suppl 1 (2004) p.i130-6 DOI: 10.1093/bioinformatics/bth948
*
A practical and robust sequence search strategy for structural genomics target selection.
Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA. Bioinformatics (Oxford, England) Volume 20 (2004) p.2288-2295 DOI: 10.1093/bioinformatics/bth240
Conformational change in substrate binding, catalysis and product release: an open and shut case?
Gutteridge A, Thornton J. FEBS letters Volume 567 (2004) p.67-73 DOI: 10.1016/j.febslet.2004.03.067
An examination of the conservation of surface patch polarity for proteins.
Shanahan HP, Thornton JM. Bioinformatics Volume 20 (2004) p.2197-2204 DOI: 10.1093/bioinformatics/bth218
Searching for functional sites in protein structures.
Jones S, Thornton JM. Current opinion in chemical biology Volume 8 (2004) p.3-7 DOI: 10.1016/j.cbpa.2003.11.001
*
Evolution of protein superfamilies and bacterial genome size.
Ranea JA, Buchan DW, Thornton JM, Orengo CA. Journal of molecular biology Volume 336 (2004) p.871-887 DOI: 10.1016/j.jmb.2003.12.044
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
Porter CT, Bartlett GJ, Thornton JM. Nucleic acids research Volume 32 (2004) p.D129-33 DOI: 10.1093/nar/gkh028
*
The Proteome and the Metabolome: A Structural Perspective
Nobeli I, Thornton JM. Peptide Revolution: Genomics, Proteomics and Therapeutics American Chemical Society
*
The Metabolome
Nobeli I, Thornton JM. The Encyclopaedia of Computational Chemistry Wiley
*
X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.
Savchenko A, Skarina T, Evdokimova E, Watson JD, Laskowski R, Arrowsmith CH, Edwards AM, Joachimiak A, Zhang RG. Proteins Volume 54 (2004) p.162-165 DOI: 10.1002/prot.10585
*
Conformational Change in Substrate Binding, Catalysis and Product Release: An Open and Shut Case?
Gutteridge A, Thornton JM. FEBS letters Volume 567 (2004) p.67-73
*
Software Engineering Challenges in Bioinformatics
Barker J, Thornton JM. ICSE (2004) p.12-16

2003

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
Jones S, Shanahan HP, Berman HM, Thornton JM. Nucleic acids research Volume 31 (2003) p.7189-7198 DOI: 10.1093/nar/gfg922
A structure-based anatomy of the E.coli metabolome.
Nobeli I, Ponstingl H, Krissinel EB, Thornton JM. Journal of molecular biology Volume 334 (2003) p.697-719 DOI: 10.1016/j.jmb.2003.10.008
Molecular basis of inherited diseases: a structural perspective.
Steward RE, MacArthur MW, Laskowski RA, Thornton JM. Trends in genetics : TIG Volume 19 (2003) p.505-513 DOI: 10.1016/s0168-9525(03)00195-1
*
Recognizing the fold of a protein structure.
Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C. Bioinformatics (Oxford, England) Volume 19 (2003) p.1748-1759 DOI: 10.1093/bioinformatics/btg240
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
Barker JA, Thornton JM. Bioinformatics (Oxford, England) Volume 19 (2003) p.1644-1649 DOI: 10.1093/bioinformatics/btg226
*
Estimation of weights and validation: a marginal likelihood approach.
Lebedev AA, Tickle IJ, Laskowski RA, Moss DS. Acta crystallographica. Section D, Biological crystallography Volume 59 (2003) p.1557-1566 DOI: 10.1107/s0907444903014367
*
A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
Dawe JH, Porter CT, Thornton JM, Tabor AB. Proteins Volume 52 (2003) p.427-435 DOI: 10.1002/prot.10421
*
Catalysing new reactions during evolution: economy of residues and mechanism.
Bartlett GJ, Borkakoti N, Thornton JM. Journal of molecular biology Volume 331 (2003) p.829-860 DOI: 10.1016/s0022-2836(03)00734-4
*
Analysis of metabolic networks using a pathway distance metric through linear programming.
Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG. Metabolic engineering Volume 5 (2003) p.211-219 DOI: 10.1016/s1096-7176(03)00043-0
Using a neural network and spatial clustering to predict the location of active sites in enzymes.
Gutteridge A, Bartlett GJ, Thornton JM. Journal of molecular biology Volume 330 (2003) p.719-734 DOI: 10.1016/s0022-2836(03)00515-1
Diversity of protein-protein interactions.
Nooren IM, Thornton JM. The EMBO journal Volume 22 (2003) p.3486-3492 DOI: 10.1093/emboj/cdg359
Using structural motif templates to identify proteins with DNA binding function.
Jones S, Barker JA, Nobeli I, Thornton JM. Nucleic acids research Volume 31 (2003) p.2811-2823 DOI: 10.1093/nar/gkg386
*
Sequences and topology.
Gerstein M, Thornton JM. Current opinion in structural biology Volume 13 (2003) p.341-343 DOI: 10.1016/s0959-440x(03)00080-0
*
Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.
Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. The Journal of biological chemistry Volume 278 (2003) p.26039-26045 DOI: 10.1074/jbc.M303867200
*
Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases.
Zhang RG, Duke N, Laskowski R, Evdokimova E, Skarina T, Edwards A, Joachimiak A, Savchenko A. Proteins Volume 51 (2003) p.311-314 DOI: 10.1002/prot.10307
Target selection and determination of function in structural genomics.
Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM. IUBMB life Volume 55 (2003) p.249-255 DOI: 10.1080/1521654031000123385
*
Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor.
Wu RY, Zhang RG, Zagnitko O, Dementieva I, Maltzev N, Watson JD, Laskowski R, Gornicki P, Joachimiak A. The Journal of biological chemistry Volume 278 (2003) p.20240-20244 DOI: 10.1074/jbc.M300292200
*
A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks.
Shepherd AJ, Gorse D, Thornton JM. Proteins Volume 50 (2003) p.290-302 DOI: 10.1002/prot.10290
*
Protein-DNA Interactions: The Story so Far and a new method for prediction
Jones S, Thornton JM. Comp. Funct. Genom (Vol 4)
From protein structure to biochemical function?
Laskowski RA, Watson JD, Thornton JM. Journal of structural and functional genomics Volume 4 (2003) p.167-177 DOI: 10.1023/a:1026127927612
*
The CATH database: an extended protein family resource for structural and functional genomics.
Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA. Nucleic acids research Volume 31 (2003) p.452-455 DOI: 10.1093/nar/gkg062
*
Inferring protein function from structure.
Bartlett GJ, Todd AE, Thornton JM. Methods of biochemical analysis Volume 44 (2003) p.387-407
*
Gene3D: structural assignments for the biologist and bioinformaticist alike.
Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. Nucleic acids research Volume 31 (2003) p.469-473 DOI: 10.1093/nar/gkg051
Protein-DNA interactions: the story so far and a new method for prediction.
Jones S, Thornton JM. Comparative and functional genomics Volume 4 (2003) p.428-431 DOI: 10.1002/cfg.303
*
Proteomics: The Protein Complement of the Genome
Ponstingl H, Thornton JM. The biochemist Volume 25 (2003) p.7-9
*
The CATH domain structure database.
Orengo CA, Pearl FM, Thornton JM. Methods of biochemical analysis Volume 44 (2003) p.249-271
*
The Proteome and the Metabolome
Thornton JM, Nobeli I. Biopolymers Volume 71 (2003) p.281
Structural characterisation and functional significance of transient protein-protein interactions.
Nooren IM, Thornton JM. Journal of molecular biology Volume 325 (2003) p.991-1018 DOI: 10.1016/s0022-2836(02)01281-0
*
Diversity of Protein-Protein Interactions
Nooren I, Thornton JM. EMBO Journal (22 edition)

2002

Bioinformatics and protein design.
Laskowski RA, Chan AW. Current pharmaceutical biotechnology Volume 3 (2002) p.317-327 DOI: 10.2174/1389201023378157
*
Analysis of catalytic residues in enzyme active sites.
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM. Journal of molecular biology Volume 324 (2002) p.105-121 DOI: 10.1016/s0022-2836(02)01036-7
*
Quantifying the similarities within fold space.
Harrison A, Pearl F, Mott R, Thornton J, Orengo C. Journal of molecular biology Volume 323 (2002) p.909-926 DOI: 10.1016/s0022-2836(02)00992-0
*
Sequence and structural differences between enzyme and nonenzyme homologs.
Todd AE, Orengo CA, Thornton JM. Structure (London, England : 1993) Volume 10 (2002) p.1435-1451 DOI: 10.1016/s0969-2126(02)00861-4
*
Toward predicting protein topology: an approach to identifying beta hairpins.
de la Cruz X, Hutchinson EG, Shepherd A, Thornton JM. Proceedings of the National Academy of Sciences of the United States of America Volume 99 (2002) p.11157-11162 DOI: 10.1073/pnas.162376199
Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
Steward RE, Thornton JM. Proteins Volume 48 (2002) p.178-191 DOI: 10.1002/prot.10152
*
Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.
Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Joachimiak A, Edwards A, Savchenko A. Proteins Volume 48 (2002) p.427-430 DOI: 10.1002/prot.10160
*
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
Nagano N, Orengo CA, Thornton JM. Journal of molecular biology Volume 321 (2002) p.741-765 DOI: 10.1016/s0022-2836(02)00649-6
*
Plasticity of enzyme active sites.
Todd AE, Orengo CA, Thornton JM. Trends in biochemical sciences Volume 27 (2002) p.419-426 DOI: 10.1016/s0968-0004(02)02158-8
*
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Luscombe NM, Thornton JM. Journal of molecular biology Volume 320 (2002) p.991-1009 DOI: 10.1016/s0022-2836(02)00571-5
*
The CCPN project: an interim report on a data model for the NMR community.
Fogh R, Ionides J, Ulrich E, Boucher W, Vranken W, Linge JP, Habeck M, Rieping W, Bhat TN, Westbrook J, Henrick K, Gilliland G, Berman H, Thornton J, Nilges M, Markley J, Laue E. Nature structural biology Volume 9 (2002) p.416-418 DOI: 10.1038/nsb0602-416
*
Pathway evolution, structurally speaking.
Rison SC, Thornton JM. Current opinion in structural biology Volume 12 (2002) p.374-382 DOI: 10.1016/s0959-440x(02)00331-7
*
Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.
Rison SC, Teichmann SA, Thornton JM. Journal of molecular biology Volume 318 (2002) p.911-932 DOI: 10.1016/s0022-2836(02)00140-7
*
Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
Zhang RG, Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Edwards A, Joachimiak A, Savchenko A. The Journal of biological chemistry Volume 277 (2002) p.19183-19190 DOI: 10.1074/jbc.M112171200
*
RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast prion [URE3].
Sekito T, Liu Z, Thornton J, Butow RA. Molecular biology of the cell Volume 13 (2002) p.795-804 DOI: 10.1091/mbc.01-09-0473
*
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA. Genome research Volume 12 (2002) p.503-514 DOI: 10.1101/gr.213802
*
Wavelet transforms for the characterization and detection of repeating motifs.
Murray KB, Gorse D, Thornton JM. Journal of molecular biology Volume 316 (2002) p.341-363 DOI: 10.1006/jmbi.2001.5332
*
Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein.
Martin AC, Facchiano AM, Cuff AL, Hernandez-Boussard T, Olivier M, Hainaut P, Thornton JM. Human mutation Volume 19 (2002) p.149-164 DOI: 10.1002/humu.10032
*
Automatic Interence of Protein Quatenary Structure from Crystals
Ponstingl H, Kabir T, Thornton JM. Journal of applied crystallography Volume 36 (2002) p.1116-1122
*
Proteins, Small Molecules and Networks
Nobeli I, Thornton JM. QSAR Proceedings 2002
*
PROCHECK: Validation of Protein Structure Coordinates
Laskowski RA, MacArthur MW, Thornton JM. International Tables for Crytallography Kluwer Academic Publishers, Netherlands (Vol. F)
*
The CATH protein family database: a resource for structural and functional annotation of genomes.
Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM. Proteomics Volume 2 (2002) p.11-21 DOI: 10.1002/1615-9861(200201)2:1<11::aid-prot11>3.3.co;2-k

2001

*
Small-molecule metabolism: an enzyme mosaic.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C. Trends in biotechnology Volume 19 (2001) p.482-486 DOI: 10.1016/s0167-7799(01)01813-3
*
On the molecular discrimination between adenine and guanine by proteins.
Nobeli I, Laskowski RA, Valdar WS, Thornton JM. Nucleic acids research Volume 29 (2001) p.4294-4309 DOI: 10.1093/nar/29.21.4294
*
The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
Nagano N, Porter CT, Thornton JM. Protein engineering Volume 14 (2001) p.845-855 DOI: 10.1093/protein/14.11.845
*
Conservation helps to identify biologically relevant crystal contacts.
Valdar WS, Thornton JM. Journal of molecular biology Volume 313 (2001) p.399-416 DOI: 10.1006/jmbi.2001.5034
*
The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C. Journal of molecular biology Volume 311 (2001) p.693-708 DOI: 10.1006/jmbi.2001.4912
*
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
Luscombe NM, Laskowski RA, Thornton JM. Nucleic acids research Volume 29 (2001) p.2860-2874 DOI: 10.1093/nar/29.13.2860
*
From genome to function.
Thornton JM. Science (New York, N.Y.) Volume 292 (2001) p.2095-2097 DOI: 10.1126/science.292.5524.2095
*
Evolution of function in protein superfamilies, from a structural perspective.
Todd AE, Orengo CA, Thornton JM. Journal of molecular biology Volume 307 (2001) p.1113-1143 DOI: 10.1006/jmbi.2001.4513
*
Protein-RNA interactions: a structural analysis.
Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM. Nucleic acids research Volume 29 (2001) p.943-954 DOI: 10.1093/nar/29.4.943
*
Structural genomics takes off.
Thornton J. Trends in biochemical sciences Volume 26 (2001) p.88-89 DOI: 10.1016/s0968-0004(00)01765-5
*
A rapid classification protocol for the CATH Domain Database to support structural genomics.
Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA. Nucleic acids research Volume 29 (2001) p.223-227 DOI: 10.1093/nar/29.1.223
*
Evaluation of a Knowledge-Based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes
Nobeli I, Mitchell JM, Alex A, Thornton JM. Journal of computational chemistry Volume 22 (2001) p.673-688 DOI: 10.1002/jcc.1036
*
Playing with Proteins
Thornton JM. Chemistry in Britain (Vol. 37)
*
The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution.
Thornton JM. Protein science : a publication of the Protein Society Volume 10 (2001) p.3-11 DOI: 10.1110/ps.90001
*
Structural Genomics Takes off
Thornton JM. Trends in Biochemical Sciences (Vol. 26)
*
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
Valdar WS, Thornton JM. Proteins Volume 42 (2001) p.108-124 DOI: 10.1002/1097-0134(20010101)42:1<108::aid-prot110>3.0.co;2-o

2000

*
From structure to function: approaches and limitations.
Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA. Nature structural biology Volume 7 Suppl (2000) p.991-994 DOI: 10.1038/80784
Discriminating between homodimeric and monomeric proteins in the crystalline state.
Ponstingl H, Henrick K, Thornton JM. Proteins Volume 41 (2000) p.47-57 DOI: 10.1002/1097-0134(20001001)41:1<47::aid-prot80>3.3.co;2-#
*
An overview of the structures of protein-DNA complexes.
Luscombe NM, Austin SE, Berman HM, Thornton JM. Genome biology Volume 1 (2000) p.REVIEWS001 DOI: 10.1186/gb-2000-1-1-reviews001
*
Comparison of functional annotation schemes for genomes.
Rison SC, Hodgman TC, Thornton JM. Functional & integrative genomics Volume 1 (2000) p.56-69 DOI: 10.1007/s101420000005
*
The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.
Bray JE, Todd AE, Pearl FM, Thornton JM, Orengo CA. Protein engineering Volume 13 (2000) p.153-165 DOI: 10.1093/protein/13.3.153
*
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.
Jones S, Marin A, Thornton JM. Protein engineering Volume 13 (2000) p.77-82 DOI: 10.1093/protein/13.2.77
*
Analysis and prediction of carbohydrate binding sites.
Taroni C, Jones S, Thornton JM. Protein engineering Volume 13 (2000) p.89-98 DOI: 10.1093/protein/13.2.89
*
Using the CATH domain database to assign structures and functions to the genome sequences.
Pearl F, Todd AE, Bray JE, Martin AC, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA. Biochemical Society transactions Volume 28 (2000) p.269-275 DOI: 10.1042/bst0280269
*
Assigning genomic sequences to CATH.
Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA. Nucleic acids research Volume 28 (2000) p.277-282 DOI: 10.1093/nar/28.1.277

1999

*
Evolution of protein function, from a structural perspective.
Todd AE, Orengo CA, Thornton JM. Current opinion in chemical biology Volume 3 (1999) p.548-556 DOI: 10.1016/s1367-5931(99)00007-1
*
Protein folds, functions and evolution.
Thornton JM, Orengo CA, Todd AE, Pearl FM. Journal of molecular biology Volume 293 (1999) p.333-342 DOI: 10.1006/jmbi.1999.3054
*
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
Nagano N, Hutchinson EG, Thornton JM. Protein science : a publication of the Protein Society Volume 8 (1999) p.2072-2084 DOI: 10.1110/ps.8.10.2072
*
From protein structure to function.
Orengo CA, Todd AE, Thornton JM. Current opinion in structural biology Volume 9 (1999) p.374-382 DOI: 10.1016/s0959-440x(99)80051-7
*
COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.
Harding SE, Horton JC, Jones S, Thornton JM, Winzor DJ. Biophysical journal Volume 76 (1999) p.2432-2438 DOI: 10.1016/s0006-3495(99)77398-4
*
Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?
MacArthur MW, Thornton JM. Acta Crystallographica Section D: Biological Crystallography Volume 55 (1999) p.994-1004 DOI: 10.1107/s0907444999002231
*
Prediction of the location and type of beta-turns in proteins using neural networks.
Shepherd AJ, Gorse D, Thornton JM. Protein Science : A Publication of the Protein Society Volume 8 (1999) p.1045-1055 DOI: 10.1110/ps.8.5.1045
*
DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.
Todd AE, Orengo CA, Thornton JM. Protein engineering Volume 12 (1999) p.375-379 DOI: 10.1093/protein/12.5.375
*
Correlation of observed fold frequency with the occurrence of local structural motifs.
Salem GM, Hutchinson EG, Orengo CA, Thornton JM. Journal of molecular biology Volume 287 (1999) p.969-981 DOI: 10.1006/jmbi.1999.2642
Protein structural topology: Automated analysis and diagrammatic representation.
Westhead DR, Slidel TW, Flores TP, Thornton JM. Protein Science : A Publication of the Protein Society Volume 8 (1999) p.897-904 DOI: 10.1110/ps.8.4.897
*
Motif-based searching in TOPS protein topology databases.
Gilbert D, Westhead D, Nagano N, Thornton J. Bioinformatics (Oxford, England) Volume 15 (1999) p.317-326 DOI: 10.1093/bioinformatics/15.4.317
*
Protein-DNA interactions: A structural analysis.
Jones S, van Heyningen P, Berman HM, Thornton JM. Journal of molecular biology Volume 287 (1999) p.877-896 DOI: 10.1006/jmbi.1999.2659
*
Factors limiting the performance of prediction-based fold recognition methods.
de la Cruz X, Thornton JM. Protein science : a publication of the Protein Society Volume 8 (1999) p.750-759 DOI: 10.1110/ps.8.4.750
*
Three-dimensional structure analysis of PROSITE patterns.
Kasuya A, Thornton JM. Journal of molecular biology Volume 286 (1999) p.1673-1691 DOI: 10.1006/jmbi.1999.2581
*
BLEEP - A Potential of Mean Force Describing Protein-Ligan Interactions: Generating the Potential
Mitchell JBO, Laskowski RA, Alex A, Thornton JM. Journal of computational chemistry Volume 20 (1999) p.11
*
Software Tools for Protein Structure Analysis and Fold Classification
Thornton JM, Mitchie AD, Hutchinson EG, Laskowski RA, Orengo CA.
*
The CATH Database provides insights into protein structure/function relationships.
Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM. Nucleic acids research Volume 27 (1999) p.275-279 DOI: 10.1093/nar/27.1.275

1998

*
Determinants of strand register in antiparallel beta-sheets of proteins.
Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN. Protein science : a publication of the Protein Society Volume 7 (1998) p.2287-2300 DOI: 10.1002/pro.5560071106
*
Contemporary approaches to protein structure classification.
Swindells MB, Orengo CA, Jones DT, Hutchinson EG, Thornton JM. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 20 (1998) p.884-891 DOI: 10.1002/(sici)1521-1878(199811)20:11<884::aid-bies3>3.0.co;2-h
*
Iditis: protein structure database.
Gardner S, Thornton J. Acta Crystallographica Section D: Biological Crystallography Volume 54 (1998) p.1071-1077 DOI: 10.1107/s0907444998007112
*
Classifying a protein in the CATH database of domain structures.
Orengo CA, Martin AM, Hutchinson G, Jones S, Jones DT, Michie AD, Swindells MB, Thornton JM. Acta Crystallographica Section D: Biological Crystallography Volume 54 (1998) p.1155-1167 DOI: 10.1107/s0907444998007501
*
New tools and resources for analysing protein structures and their interactions.
Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou M, Thornton JM. Acta crystallographica. Section D, Biological crystallography Volume 54 (1998) p.1132-1138 DOI: 10.1107/s0907444998007318
*
Validation of protein models derived from experiment.
Laskowski RA, MacArthur MW, Thornton JM. Current opinion in structural biology Volume 8 (1998) p.631-639 DOI: 10.1016/s0959-440x(98)80156-5
*
Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
Milburn D, Laskowski RA, Thornton JM. Protein engineering Volume 11 (1998) p.855-859 DOI: 10.1093/protein/11.10.855
PQS: a protein quaternary structure file server.
Henrick K, Thornton JM. Trends in biochemical sciences Volume 23 (1998) p.358-361 DOI: 10.1016/s0968-0004(98)01253-5
*
1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins.
Bloch C, Patel SU, Baud F, Zvelebil MJ, Carr MD, Sadler PJ, Thornton JM. Proteins Volume 32 (1998) p.334-349 DOI: 10.1002/(sici)1097-0134(19980815)32:3<334::aid-prot9>3.0.co;2-h
Protein structure prediction.
Westhead DR, Thornton JM. Current opinion in biotechnology Volume 9 (1998) p.383-389 DOI: 10.1016/s0958-1669(98)80012-8
*
Protein folds and functions.
Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM. Structure (London, England : 1993) Volume 6 (1998) p.875-884 DOI: 10.1016/s0969-2126(98)00089-6
*
Design, synthesis and structure of a zinc finger with an artificial beta-turn.
Viles JH, Patel SU, Mitchell JB, Moody CM, Justice DE, Uppenbrink J, Doyle PM, Harris CJ, Sadler PJ, Thornton JM. Journal of molecular biology Volume 279 (1998) p.973-986 DOI: 10.1006/jmbi.1998.1764
*
Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.
Zuccotto F, Martin AC, Laskowski RA, Thornton JM, Gilbert IH. Journal of computer-aided molecular design Volume 12 (1998) p.241-257 DOI: 10.1023/a:1016085005275
*
Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
Hubbard SJ, Beynon RJ, Thornton JM. Protein engineering Volume 11 (1998) p.349-359 DOI: 10.1093/protein/11.5.349
*
Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage.
Smith GP, Patel SU, Windass JD, Thornton JM, Winter G, Griffiths AD. Journal of molecular biology Volume 277 (1998) p.317-332 DOI: 10.1006/jmbi.1997.1621
*
Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.
Journal of molecular biology Volume 276 (1998) p.417-436
*
Domain assignment for protein structures using a consensus approach: characterization and analysis.
Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM. Protein science : a publication of the Protein Society Volume 7 (1998) p.233-242 DOI: 10.1002/pro.5560070202
*
Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).
Patel SU, Osborn R, Rees S, Thornton JM. Biochemistry Volume 37 (1998) p.983-990 DOI: 10.1021/bi971747d
*
Pattern Search over the TOPS Protein Topology Database
Gilbert DR, Westhead DR, Hatton DC, Thornton JM. Protein Data Bank Quarterly Newsletter Volume 85 (1998) p.7-9
*
The Future of Bioinformatics
Thornton JM. Trends Guide to Bioinformatics
An atlas of protein topology cartoons available on the World-Wide Web.
Westhead DR, Hatton DC, Thornton JM. Trends in biochemical sciences Volume 23 (1998) p.35-36 DOI: 10.1016/s0968-0004(97)01161-4

1997

*
PDBsum: a Web-based database of summaries and analyses of all PDB structures.
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM. Trends in biochemical sciences Volume 22 (1997) p.488-490 DOI: 10.1016/s0968-0004(97)01140-7
*
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Luscombe NM, Laskowski RA, Thornton JM. Nucleic acids research Volume 25 (1997) p.4940-4945 DOI: 10.1093/nar/25.24.4940
*
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
Wallace AC, Borkakoti N, Thornton JM. Protein science : a publication of the Protein Society Volume 6 (1997) p.2308-2323 DOI: 10.1002/pro.5560061104
*
Non-randomness in side-chain packing: the distribution of interplanar angles.
Mitchell JB, Laskowski RA, Thornton JM. Proteins Volume 29 (1997) p.370-380 DOI: 10.1002/(sici)1097-0134(199711)29:3<370::aid-prot10>3.0.co;2-k
*
Analysis of protein-protein interaction sites using surface patches.
Jones S, Thornton JM. Journal of molecular biology Volume 272 (1997) p.121-132 DOI: 10.1006/jmbi.1997.1234
*
Prediction of protein-protein interaction sites using patch analysis.
Jones S, Thornton JM. Journal of molecular biology Volume 272 (1997) p.133-143 DOI: 10.1006/jmbi.1997.1233
*
Modelling protein unfolding: hen egg-white lysozyme.
Williams MA, Thornton JM, Goodfellow JM. Protein engineering Volume 10 (1997) p.895-903 DOI: 10.1093/protein/10.8.895
*
CATH--a hierarchic classification of protein domain structures.
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. Structure (London, England : 1993) Volume 5 (1997) p.1093-1108 DOI: 10.1016/s0969-2126(97)00260-8
*
Computational Approaches to Protein Ligand Interactions: Protein-heme Complexes
Karmirantzou MI, Thornton JM. Rational Molecular Design in Drug Research: Alfred Benzon Symposium 42
*
Assessment of comparative modeling in CASP2.
Martin AC, MacArthur MW, Thornton JM. Proteins Volume Suppl 1 (1997) p.14-28 DOI: 10.1002/(sici)1097-0134(1997)1+<14::aid-prot4>3.3.co;2-f
*
Structures of N-termini of helices in proteins.
Doig AJ, MacArthur MW, Stapley BJ, Thornton JM. Protein science : a publication of the Protein Society Volume 6 (1997) p.147-155 DOI: 10.1002/pro.5560060117

1996

*
Deviations from planarity of the peptide bond in peptides and proteins.
MacArthur MW, Thornton JM. Journal of molecular biology Volume 264 (1996) p.1180-1195 DOI: 10.1006/jmbi.1996.0705
*
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM. Journal of biomolecular NMR Volume 8 (1996) p.477-486 DOI: 10.1007/bf00228148
*
Protein clefts in molecular recognition and function.
Laskowski RA, Luscombe NM, Swindells MB, Thornton JM. Protein science : a publication of the Protein Society Volume 5 (1996) p.2438-2452 DOI: 10.1002/pro.5560051206
*
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.
Viles JH, Mitchell JB, Gough SL, Doyle PM, Harris CJ, Sadler PJ, Thornton JM. European journal of biochemistry Volume 242 (1996) p.352-362 DOI: 10.1111/j.1432-1033.1996.0352r.x
*
Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.
Martin AC, Thornton JM. Journal of molecular biology Volume 263 (1996) p.800-815 DOI: 10.1006/jmbi.1996.0617
*
Protein recognition of adenylate: an example of a fuzzy recognition template.
Moodie SL, Mitchell JB, Thornton JM. Journal of molecular biology Volume 263 (1996) p.486-500 DOI: 10.1006/jmbi.1996.0591
*
Antibody-antigen interactions: contact analysis and binding site topography.
MacCallum RM, Martin AC, Thornton JM. Journal of molecular biology Volume 262 (1996) p.732-745 DOI: 10.1006/jmbi.1996.0548
*
Analysis of domain structural class using an automated class assignment protocol.
Michie AD, Orengo CA, Thornton JM. Journal of molecular biology Volume 262 (1996) p.168-185 DOI: 10.1006/jmbi.1996.0506
*
Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.
Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J. Trends in biochemical sciences Volume 21 (1996) p.251-256 DOI: 10.1016/s0968-0004(96)10037-2
*
Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic.
Doyle PM, Harris JC, Moody CM, Sadler PJ, Sims M, Thornton JM, Uppenbrink J, Viles JH. International journal of peptide and protein research Volume 47 (1996) p.427-436
*
Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.
Wallace AC, Laskowski RA, Thornton JM. Protein science : a publication of the Protein Society Volume 5 (1996) p.1001-1013 DOI: 10.1002/pro.5560050603
*
X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.
Laskowski RA, Thornton JM, Humblet C, Singh J. Journal of molecular biology Volume 259 (1996) p.175-201 DOI: 10.1006/jmbi.1996.0311
*
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.
Jones DT, Moody CM, Uppenbrink J, Viles JH, Doyle PM, Harris CJ, Pearl LH, Sadler PJ, Thornton JM. Proteins Volume 24 (1996) p.502-513 DOI: 10.1002/(sici)1097-0134(199604)24:4<502::aid-prot9>3.0.co;2-f
*
Potential energy functions for threading.
Jones DT, Thornton JM. Current opinion in structural biology Volume 6 (1996) p.210-216 DOI: 10.1016/s0959-440x(96)80076-5
*
Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA.
Kalsi JK, Martin AC, Hirabayashi Y, Ehrenstein M, Longhurst CM, Ravirajan C, Zvelebil M, Stollar BD, Thornton JM, Isenberg DA. Molecular immunology Volume 33 (1996) p.471-483 DOI: 10.1016/0161-5890(95)00138-7
*
PROMOTIF--a program to identify and analyze structural motifs in proteins.
Hutchinson EG, Thornton JM. Protein science : a publication of the Protein Society Volume 5 (1996) p.212-220 DOI: 10.1002/pro.5560050204
*
Molecular recognition by proteins: protein-ligand interactions from a structural perspective.
Wallace AC, Laskowski RA, Singh J, Thornton JM. Biochemical Society transactions Volume 24 (1996) p.280-284 DOI: 10.1042/bst0240280
*
Principles of protein-protein interactions.
Jones S, Thornton JM. Proceedings of the National Academy of Sciences of the United States of America Volume 93 (1996) p.13-20 DOI: 10.1073/pnas.93.1.13
*
Protein fold recognition by sequence threading: tools and assessment techniques.
Miller RT, Jones DT, Thornton JM. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 10 (1996) p.171-178 DOI: 10.1096/fasebj.10.1.8566539
*
Molecular Recogntion by Proteins - Protein-Ligand Interactions from a Structural Perspective
Wallace AC, Laskowski RA, Singh J, Thornton JM. Biochemical Society Transactions (Vol. 24)
*
Chirality in Protein Structure
Slidel TWF, Thornton JM. Protein Folds: A Distance Based Approach CRC Press (1st Ed.)
*
Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM. Journal of molecular biology Volume 255 (1996) p.494-506 DOI: 10.1006/jmbi.1996.0041

1995

*
Long loops in proteins.
Martin AC, Toda K, Stirk HJ, Thornton JM. Protein engineering Volume 8 (1995) p.1093-1101 DOI: 10.1093/protein/8.11.1093
*
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Jones DT, Miller RT, Thornton JM. Proteins Volume 23 (1995) p.387-397 DOI: 10.1002/prot.340230312
*
Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity.
Orengo CA, Swindells MB, Michie AD, Zvelebil MJ, Driscoll PC, Waterfield MD, Thornton JM. Protein science : a publication of the Protein Society Volume 4 (1995) p.1977-1983 DOI: 10.1002/pro.5560041003
*
Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.
Swindells MB, MacArthur MW, Thornton JM. Nature structural biology Volume 2 (1995) p.596-603 DOI: 10.1038/nsb0795-596
*
Protein folds: towards understanding folding from inspection of native structures.
Thornton JM, Jones DT, MacArthur MW, Orengo CM, Swindells MB. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 348 (1995) p.71-79 DOI: 10.1098/rstb.1995.0047
*
The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains.
McDonald IK, Thornton JM. Protein engineering Volume 8 (1995) p.217-224 DOI: 10.1093/protein/8.3.217
*
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Wallace AC, Laskowski RA, Thornton JM. Protein engineering Volume 8 (1995) p.127-134 DOI: 10.1093/protein/8.2.127
*
Modelling the Interaction of Protein Side Chains
Mitchell JBO, Thornton JM, Price SL. Modelling of Biomolecular Structures and Mechanisms
*
Protein Engineering - Editorial Overview
Thornton JM, Berg JM. Current Opinion in Biotechnology (Vol 6)
*
Software Tools for Protein Structure Analysis and Fold Classification
Michie AD, Hutchinson EG, Laskowski RA, Orengo CM, Thornton JM. CCP4 Meeting "Getting the Most from your Model"
*
Protein-protein interactions: a review of protein dimer structures.
Jones S, Thornton JM. Progress in biophysics and molecular biology Volume 63 (1995) p.31-65 DOI: 10.1016/0079-6107(94)00008-w
*
Folding of Beta Structure in Proteins
Evans PA, Gladwin ST, Gopalakrishnan B, Tisi LC, Woolfson DN, Murracy JH, Packman LC, Trotter BW, Mackay JP, Williams DH, Thornton JM. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 9 (1995) p.A1239
*
Chirality in Proteins
Slidel TMW, Thornton JM. Protein Folds: A Distance Based Approach CRC Press
*
Protein Folds and Folding
Thornton JM, Jones DT, MacArthur M, Orengo CA, Swindells M. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 9 (1995) p.A1240

1994

*
A revised set of potentials for beta-turn formation in proteins.
Hutchinson EG, Thornton JM. Protein science : a publication of the Protein Society Volume 3 (1994) p.2207-2216 DOI: 10.1002/pro.5560031206
*
Protein superfamilies and domain superfolds.
Orengo CA, Jones DT, Thornton JM. Nature Volume 372 (1994) p.631-634 DOI: 10.1038/372631a0
*
Buried waters and internal cavities in monomeric proteins.
Williams MA, Goodfellow JM, Thornton JM. Protein science : a publication of the Protein Society Volume 3 (1994) p.1224-1235 DOI: 10.1002/pro.5560030808
*
Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
Mitchell JB, Nandi CL, McDonald IK, Thornton JM, Price SL. Journal of molecular biology Volume 239 (1994) p.315-331 DOI: 10.1006/jmbi.1994.1370
*
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Hubbard SJ, Eisenmenger F, Thornton JM. Protein science : a publication of the Protein Society Volume 3 (1994) p.757-768 DOI: 10.1002/pro.5560030505
*
NMR and crystallography--complementary approaches to structure determination.
MacArthur MW, Driscoll PC, Thornton JM. Trends in biotechnology Volume 12 (1994) p.149-153 DOI: 10.1016/0167-7799(94)90074-4
*
Satisfying hydrogen bonding potential in proteins.
McDonald IK, Thornton JM. Journal of molecular biology Volume 238 (1994) p.777-793 DOI: 10.1006/jmbi.1994.1334
*
A model recognition approach to the prediction of all-helical membrane protein structure and topology.
Jones DT, Taylor WR, Thornton JM. Biochemistry Volume 33 (1994) p.3038-3049 DOI: 10.1021/bi00176a037
*
A mutation data matrix for transmembrane proteins.
Jones DT, Taylor WR, Thornton JM. FEBS letters Volume 339 (1994) p.269-275 DOI: 10.1016/0014-5793(94)80429-x
*
Protein Motifs and Folding Recognition
Thornton JM, Orengo CM, Jones DT, Taylor WR. Biophysical journal Volume 66 (1994) p.A241
*
An algorithm for automatically generating protein topology cartoons.
Flores TP, Moss DS, Thornton JM. Protein engineering Volume 7 (1994) p.31-37 DOI: 10.1093/protein/7.1.31
*
Evaluation of Protein Coordinate Data Sets
Laskowski RA, MacArthur MW, Thornton JM. Proc. CCP4 Study Weekend
*
The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.
Stirk HJ, Thornton JM. Protein engineering Volume 7 (1994) p.47-56 DOI: 10.1093/protein/7.1.47
*
Knowledge-based validation of protein-structure coordinates derived by x-ray Cyrstallography and NMR-Spectroscopy
MacArthur MW, Laskowski RA, Thornton JM. Current Opinion in Structural Biology (Vol 4)