Gemma Holliday - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 

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

Year Citation  Score
2019 Ribeiro AJM, Tyzack JD, Borkakoti N, Holliday GL, Thornton JM. A global analysis of function and conservation of catalytic residues in enzymes. The Journal of Biological Chemistry. PMID 31796628 DOI: 10.1074/jbc.REV119.006289  1
2017 Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Research. PMID 29106569 DOI: 10.1093/nar/gkx1012  1
2016 Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Research. PMID 27899635 DOI: 10.1093/nar/gkw1107  1
2016 Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinformatics (Oxford, England). PMID 27153692 DOI: 10.1093/bioinformatics/btw096  1
2015 Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, et al. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database : the Journal of Biological Databases and Curation. 2015: bav063. PMID 26284514 DOI: 10.1093/database/bav063  1
2015 Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database : the Journal of Biological Databases and Curation. 2015: bav043. PMID 25957950 DOI: 10.1093/database/bav043  1
2015 Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, et al. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 83: 1005-13. PMID 25820941 DOI: 10.1002/prot.24803  1
2015 Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB. [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry. 54: 1807-18. PMID 25654171 DOI: 10.1021/bi501205e  1
2014 Holliday GL, Rahman SA, Furnham N, Thornton JM. Exploring the biological and chemical complexity of the ligases. Journal of Molecular Biology. 426: 2098-111. PMID 24657765 DOI: 10.1016/j.jmb.2014.03.008  1
2014 Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM. EC-BLAST: a tool to automatically search and compare enzyme reactions. Nature Methods. 11: 171-4. PMID 24412978 DOI: 10.1038/nmeth.2803  1
2014 Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Research. 42: D485-9. PMID 24319146 DOI: 10.1093/nar/gkt1243  1
2014 Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, ... ... Holliday GL, et al. The Structure-Function Linkage Database. Nucleic Acids Research. 42: D521-30. PMID 24271399 DOI: 10.1093/nar/gkt1130  1
2013 Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, et al. The EBI enzyme portal. Nucleic Acids Research. 41: D773-80. PMID 23175605 DOI: 10.1093/nar/gks1112  1
2012 Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM. Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. Plos Computational Biology. 8: e1002403. PMID 22396634 DOI: 10.1371/journal.pcbi.1002403  1
2012 Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Research. 40: D783-9. PMID 22058127 DOI: 10.1093/nar/gkr799  1
2012 Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM. FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Research. 40: D776-82. PMID 22006843 DOI: 10.1093/nar/gkr852  1
2011 Holliday GL, Fischer JD, Mitchell JB, Thornton JM. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. The Febs Journal. 278: 3835-45. PMID 21605342 DOI: 10.1111/j.1742-4658.2011.08190.x  1
2010 Fischer JD, Holliday GL, Rahman SA, Thornton JM. The structures and physicochemical properties of organic cofactors in biocatalysis. Journal of Molecular Biology. 403: 803-24. PMID 20850456 DOI: 10.1016/j.jmb.2010.09.018  1
2010 Fischer JD, Holliday GL, Thornton JM. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics (Oxford, England). 26: 2496-7. PMID 20679331 DOI: 10.1093/bioinformatics/btq442  1
2009 Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Small Molecule Subgraph Detector (SMSD) toolkit. Journal of Cheminformatics. 1: 12. PMID 20298518 DOI: 10.1186/1758-2946-1-12  1
2009 Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. Journal of Molecular Biology. 390: 560-77. PMID 19447117 DOI: 10.1016/j.jmb.2009.05.015  1
2009 Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics (Oxford, England). 25: 2088-9. PMID 19369503 DOI: 10.1093/bioinformatics/btp256  1
2008 Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 13: 1205-18. PMID 18604568 DOI: 10.1007/s00775-008-0404-5  1
2007 Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ. Evolution of enzymes and pathways for the biosynthesis of cofactors. Natural Product Reports. 24: 972-87. PMID 17898893 DOI: 10.1039/b703107f  1
2007 Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. The chemistry of protein catalysis. Journal of Molecular Biology. 372: 1261-77. PMID 17727879 DOI: 10.1016/j.jmb.2007.07.034  1
2007 Torrance JW, Holliday GL, Mitchell JB, Thornton JM. The geometry of interactions between catalytic residues and their substrates. Journal of Molecular Biology. 369: 1140-52. PMID 17466330 DOI: 10.1016/j.jmb.2007.03.055  1
2007 O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. Using reaction mechanism to measure enzyme similarity. Journal of Molecular Biology. 368: 1484-99. PMID 17400244 DOI: 10.1016/j.jmb.2007.02.065  1
2007 Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Research. 35: D515-20. PMID 17082206 DOI: 10.1093/nar/gkl774  1
2006 Holliday GL, Murray-Rust P, Rzepa HS. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. Journal of Chemical Information and Modeling. 46: 145-57. PMID 16426051 DOI: 10.1021/ci0502698  1
2005 Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. MACiE: a database of enzyme reaction mechanisms. Bioinformatics (Oxford, England). 21: 4315-6. PMID 16188925 DOI: 10.1093/bioinformatics/bti693  1
2004 Holliday GL, Mitchell JBO, Murray-Rust P. CMLSnap: Animated reaction mechanisms Internet Journal of Chemistry. 7.  1
2002 Clarke ML, Holliday GL, Slawin AMZ, Woollins JD. Highly electron rich alkyl- and dialkyl-N-pyrrolidinyl phosphines: An evaluation of their electronic and structural properties Journal of the Chemical Society, Dalton Transactions. 1093-1103.  1
2001 Clarke ML, Holliday GL, Slawin AMZ, Derek Woollins J. First examples of M-Se-P-N-N heterocycles Inorganic Chemistry Communications. 4: 115-118. DOI: 10.1016/S1387-7003(00)00217-3  1
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