Publications by authors named "Janet M Thornton"

100Publications

In conversation with Janet Thornton.

FEBS J 2020 Oct;287(19):4106-4113

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1111/febs.15567DOI Listing
October 2020

Temporal changes in the gene expression heterogeneity during brain development and aging.

Sci Rep 2020 03 5;10(1):4080. Epub 2020 Mar 5.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1038/s41598-020-60998-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058021PMC
March 2020

A global analysis of function and conservation of catalytic residues in enzymes.

J Biol Chem 2020 01 3;295(2):314-324. Epub 2019 Dec 3.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1074/jbc.REV119.006289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956550PMC
January 2020

Identifying pseudoenzymes using functional annotation: pitfalls of common practice.

FEBS J 2020 Oct 5;287(19):4128-4140. Epub 2019 Dec 5.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1111/febs.15142DOI Listing
October 2020

Exploring Chemical Biosynthetic Design Space with Transform-MinER.

ACS Synth Biol 2019 11 5;8(11):2494-2506. Epub 2019 Nov 5.

European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton CB10 1SD , United Kingdom.

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http://dx.doi.org/10.1021/acssynbio.9b00105DOI Listing
November 2019

VarSite: Disease variants and protein structure.

Protein Sci 2020 01 27;29(1):111-119. Epub 2019 Oct 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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http://dx.doi.org/10.1002/pro.3746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933866PMC
January 2020

Emerging concepts in pseudoenzyme classification, evolution, and signaling.

Sci Signal 2019 08 13;12(594). Epub 2019 Aug 13.

Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.

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http://dx.doi.org/10.1126/scisignal.aat9797DOI Listing
August 2019

VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.

Bioinformatics 2019 11;35(22):4854-4856

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853667PMC
November 2019

The widespread increase in inter-individual variability of gene expression in the human brain with age.

Aging (Albany NY) 2019 04;11(8):2253-2280

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.18632/aging.101912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520006PMC
April 2019

Finding enzyme cofactors in Protein Data Bank.

Bioinformatics 2019 09;35(18):3510-3511

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748742PMC
September 2019

Using the drug-protein interactome to identify anti-ageing compounds for humans.

PLoS Comput Biol 2019 01 9;15(1):e1006639. Epub 2019 Jan 9.

Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1006639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342327PMC
January 2019

Identifying Potential Ageing-Modulating Drugs In Silico.

Trends Endocrinol Metab 2019 02 20;30(2):118-131. Epub 2018 Dec 20.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tem.2018.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362144PMC
February 2019

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.

Methods Mol Biol 2019 ;1851:263-275

EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-4939-8736-8_14DOI Listing
May 2019

Gene expression-based drug repurposing to target aging.

Aging Cell 2018 Oct 9;17(5):e12819. Epub 2018 Aug 9.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1111/acel.12819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156541PMC
October 2018

Transform-MinER: transforming molecules in enzyme reactions.

Bioinformatics 2018 10;34(20):3597-3599

EMBL-EBI, Wellcome Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6184704PMC
October 2018

To what extent do structural changes in catalytic metal sites affect enzyme function?

J Inorg Biochem 2018 02 8;179:40-53. Epub 2017 Nov 8.

Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.jinorgbio.2017.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760197PMC
February 2018

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

Nucleic Acids Res 2018 01;46(D1):D618-D623

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkx1012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753290PMC
January 2018

Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.

Cell Rep 2017 Oct;21(3):641-653

Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, Gower St, London WC1E 6BT, UK; Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.09.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656751PMC
October 2017

Understanding enzyme function evolution from a computational perspective.

Curr Opin Struct Biol 2017 12 8;47:131-139. Epub 2017 Sep 8.

EMBL-EBI, Wellcome Genome Campus, CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1016/j.sbi.2017.08.003DOI Listing
December 2017

PDBsum: Structural summaries of PDB entries.

Protein Sci 2018 01 27;27(1):129-134. Epub 2017 Oct 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1002/pro.3289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734310PMC
January 2018

Drug repurposing for aging research using model organisms.

Aging Cell 2017 10 16;16(5):1006-1015. Epub 2017 Jun 16.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), The Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1111/acel.12626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595691PMC
October 2017

Anna Tramontano 1957-2017.

Nat Struct Mol Biol 2017 05;24(5):431-432

Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

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http://dx.doi.org/10.1038/nsmb.3410DOI Listing
May 2017

Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.

J Mol Biol 2016 07 14;428(15):3131-46. Epub 2016 Jul 14.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981433PMC
July 2016

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Bioinformatics 2016 07 22;32(13):2065-6. Epub 2016 Feb 22.

European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btw096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920114PMC
July 2016

Exploring the chemistry and evolution of the isomerases.

Proc Natl Acad Sci U S A 2016 Feb 3;113(7):1796-801. Epub 2016 Feb 3.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

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http://dx.doi.org/10.1073/pnas.1509494113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763729PMC
February 2016

Characterising Complex Enzyme Reaction Data.

PLoS One 2016 3;11(2):e0147952. Epub 2016 Feb 3.

European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147952PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740462PMC
July 2016

Proteins: interaction at a distance.

IUCrJ 2015 Nov 30;2(Pt 6):609-10. Epub 2015 Oct 30.

European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1107/S2052252515020217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4645104PMC
November 2015

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

J Mol Biol 2016 Jan 14;428(2 Pt A):253-267. Epub 2015 Nov 14.

Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom.

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http://dx.doi.org/10.1016/j.jmb.2015.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751976PMC
January 2016

SurvCurv database and online survival analysis platform update.

Bioinformatics 2015 Dec 6;31(23):3878-80. Epub 2015 Aug 6.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653391PMC
December 2015

The Classification and Evolution of Enzyme Function.

Biophys J 2015 Sep 15;109(6):1082-6. Epub 2015 May 15.

European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.04.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576142PMC
September 2015

Longevity GWAS Using the Drosophila Genetic Reference Panel.

J Gerontol A Biol Sci Med Sci 2015 Dec 28;70(12):1470-8. Epub 2015 Apr 28.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/gerona/glv047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631106PMC
December 2015

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.

Bioinformatics 2014 Nov 26;30(21):2999-3003. Epub 2014 Jul 26.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Institute of Healthy Ageing and Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201157PMC
November 2014

The evolution of enzyme function in the isomerases.

Curr Opin Struct Biol 2014 Jun 5;26:121-30. Epub 2014 Jul 5.

European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2014.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139412PMC
June 2014

Exploring the biological and chemical complexity of the ligases.

J Mol Biol 2014 May 21;426(10):2098-111. Epub 2014 Mar 21.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.jmb.2014.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018984PMC
May 2014

EC-BLAST: a tool to automatically search and compare enzyme reactions.

Nat Methods 2014 Feb 12;11(2):171-4. Epub 2014 Jan 12.

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1038/nmeth.2803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122987PMC
February 2014

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

PLoS Comput Biol 2013 12;9(12):e1003382. Epub 2013 Dec 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861039PMC
August 2014

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Nucleic Acids Res 2014 Jan 6;42(Database issue):D485-9. Epub 2013 Dec 6.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Department of Biochemistry and Molecular Genetics, University of Virginia, 1300 Jefferson Park Ave., Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1093/nar/gkt1243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964973PMC
January 2014

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

Acta Crystallogr D Biol Crystallogr 2013 Dec 19;69(Pt 12):2395-402. Epub 2013 Nov 19.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England.

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http://dx.doi.org/10.1107/S0907444913022294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852652PMC
December 2013

PDBsum additions.

Nucleic Acids Res 2014 Jan 22;42(Database issue):D292-6. Epub 2013 Oct 22.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkt940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965036PMC
January 2014

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.

Aging Cell 2013 Oct 22;12(5):910-6. Epub 2013 Jul 22.

EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1111/acel.12121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824079PMC
October 2013

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.

Aging Cell 2013 Oct 22;12(5):917-22. Epub 2013 Jul 22.

EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1111/acel.12123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963443PMC
October 2013

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.

Mol Biosyst 2013 Jul 26;9(7):1756-64. Epub 2013 Apr 26.

EMBL-European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1039/c3mb25485bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693544PMC
July 2013

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.

PLoS One 2012 10;7(12):e50881. Epub 2012 Dec 10.

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050881PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519537PMC
June 2013

Abstracting knowledge from the Protein Data Bank.

Biopolymers 2013 Mar 29;99(3):183-8. Epub 2012 Sep 29.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1002/bip.22107DOI Listing
March 2013

Current challenges in genome annotation through structural biology and bioinformatics.

Curr Opin Struct Biol 2012 Oct 9;22(5):594-601. Epub 2012 Aug 9.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.sbi.2012.07.005DOI Listing
October 2012

ELIXIR: a distributed infrastructure for European biological data.

Trends Biotechnol 2012 May 12;30(5):241-2. Epub 2012 Mar 12.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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https://linkinghub.elsevier.com/retrieve/pii/S01677799120001
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http://dx.doi.org/10.1016/j.tibtech.2012.02.002DOI Listing
May 2012

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

Nucleic Acids Res 2012 Jan 17;40(Database issue):D776-82. Epub 2011 Oct 17.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkr852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245072PMC
January 2012

1,000 structures and more from the MCSG.

BMC Struct Biol 2011 Jan 10;11. Epub 2011 Jan 10.

Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

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http://dx.doi.org/10.1186/1472-6807-11-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024214PMC
January 2011

Computational biology for ageing.

Philos Trans R Soc Lond B Biol Sci 2011 Jan;366(1561):51-63

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1098/rstb.2010.0286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001313PMC
January 2011

The structures and physicochemical properties of organic cofactors in biocatalysis.

J Mol Biol 2010 Nov 17;403(5):803-24. Epub 2010 Sep 17.

EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1016/j.jmb.2010.09.018DOI Listing
November 2010

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

Mol Syst Biol 2010 Aug;6:399

Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK.

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http://dx.doi.org/10.1038/msb.2010.54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950082PMC
August 2010

The CoFactor database: organic cofactors in enzyme catalysis.

Bioinformatics 2010 Oct 2;26(19):2496-7. Epub 2010 Aug 2.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944199PMC
October 2010

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

Proteins 2010 Aug;78(10):2349-68

Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom.

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http://doi.wiley.com/10.1002/prot.22747
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http://dx.doi.org/10.1002/prot.22747DOI Listing
August 2010

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.

PLoS Genet 2010 Mar 19;6(3):e1000881. Epub 2010 Mar 19.

Institute of Healthy Ageing, Department of Genes, Evolution, and Environment, University College London, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1000881DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841611PMC
March 2010

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.

Proc Natl Acad Sci U S A 2010 Mar 10;107(9):4135-40. Epub 2010 Feb 10.

Department of Applied Sciences, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0910632107
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http://dx.doi.org/10.1073/pnas.0910632107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819975PMC
March 2010

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

PLoS Comput Biol 2009 Dec 4;5(12):e1000585. Epub 2009 Dec 4.

Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777313PMC
December 2009

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

Proteins 2010 Apr;78(5):1120-36

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.

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http://doi.wiley.com/10.1002/prot.22633
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http://dx.doi.org/10.1002/prot.22633DOI Listing
April 2010

Domain-ligand mapping for enzymes.

J Mol Recognit 2010 Mar-Apr;23(2):194-208

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1002/jmr.992DOI Listing
May 2010

Mapping human metabolic pathways in the small molecule chemical space.

J Chem Inf Model 2009 Oct;49(10):2272-89

Dip. Chimica e Tecnologia del Farmaco, Faculty of Pharmacy, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy.

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http://dx.doi.org/10.1021/ci900196uDOI Listing
October 2009

The (non)malignancy of cancerous amino acidic substitutions.

Proteins 2010 Feb;78(3):518-29

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://doi.wiley.com/10.1002/prot.22574
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http://dx.doi.org/10.1002/prot.22574DOI Listing
February 2010

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

Bioinformatics 2009 Dec 17;25(23):3183-4. Epub 2009 Sep 17.

Department of Applied Sciences, University of Parthenope of Naples, Centro Direzionale Isola C4 80143, Naples, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btp545DOI Listing
December 2009

Missing in action: enzyme functional annotations in biological databases.

Nat Chem Biol 2009 Aug;5(8):521-5

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1038/nchembio0809-521DOI Listing
August 2009

The fine details of evolution.

Biochem Soc Trans 2009 Aug;37(Pt 4):723-6

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1042/BST0370723DOI Listing
August 2009

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

J Mol Biol 2009 Jul 15;390(3):560-77. Epub 2009 May 15.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1016/j.jmb.2009.05.015DOI Listing
July 2009

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

Bioinformatics 2009 Aug 15;25(16):2088-9. Epub 2009 Apr 15.

Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btp256DOI Listing
August 2009

The structural basis of allosteric regulation in proteins.

FEBS Lett 2009 Jun 18;583(11):1692-8. Epub 2009 Mar 18.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1016/j.febslet.2009.03.019DOI Listing
June 2009

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.

J Mol Biol 2009 May 2;388(2):356-80. Epub 2009 Mar 2.

Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.

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http://dx.doi.org/10.1016/j.jmb.2009.02.052DOI Listing
May 2009

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

Bioinformatics 2009 May 27;25(9):1192-4. Epub 2009 Feb 27.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp116DOI Listing
May 2009

Protein promiscuity and its implications for biotechnology.

Nat Biotechnol 2009 Feb;27(2):157-67

Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK.

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http://www.nature.com/articles/nbt1519
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http://dx.doi.org/10.1038/nbt1519DOI Listing
February 2009

Small Molecule Subgraph Detector (SMSD) toolkit.

J Cheminform 2009 Aug 10;1(1):12. Epub 2009 Aug 10.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/1758-2946-1-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820491PMC
August 2009

Genome and proteome annotation: organization, interpretation and integration.

J R Soc Interface 2009 Feb;6(31):129-47

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://rsif.royalsocietypublishing.org/cgi/doi/10.1098/rsif.
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http://dx.doi.org/10.1098/rsif.2008.0341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658791PMC
February 2009

Metabolic innovations towards the human lineage.

BMC Evol Biol 2008 Sep 9;8:247. Epub 2008 Sep 9.

The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2148-8-247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553087PMC
September 2008

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

Comp Funct Genomics 2003 ;4(4):428-31

EMBL -European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1002/cfg.303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447360PMC
June 2010

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

J Biol Inorg Chem 2008 Nov 5;13(8):1205-18. Epub 2008 Jul 5.

Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.

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http://dx.doi.org/10.1007/s00775-008-0404-5DOI Listing
November 2008

Understanding the molecular machinery of genetics through 3D structures.

Nat Rev Genet 2008 Feb;9(2):141-51

European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1038/nrg2273DOI Listing
February 2008

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

J Mol Biol 2008 Jan 1;375(3):855-74. Epub 2007 Nov 1.

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.jmb.2007.10.065DOI Listing
January 2008

Evolution of binding sites for zinc and calcium ions playing structural roles.

Proteins 2008 May;71(2):813-30

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, United Kingdom.

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http://dx.doi.org/10.1002/prot.21741DOI Listing
May 2008

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.

PLoS Comput Biol 2007 Oct 27;3(10):1993-2002. Epub 2007 Aug 27.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.0030198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041975PMC
October 2007

Evolution of enzymes and pathways for the biosynthesis of cofactors.

Nat Prod Rep 2007 Oct 12;24(5):972-87. Epub 2007 Sep 12.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK CB10 1SD.

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http://dx.doi.org/10.1039/b703107fDOI Listing
October 2007

The chemistry of protein catalysis.

J Mol Biol 2007 Oct 2;372(5):1261-77. Epub 2007 Aug 2.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360700961
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http://dx.doi.org/10.1016/j.jmb.2007.07.034DOI Listing
October 2007