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Gemma Holliday, PhD

TitleEmployee of Affiliated Org.
InstitutionUniversity of California San Francisco
DepartmentBioengineering
Address1700 4th St
San Francisco CA 94158
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol. 2018; 606:1-71. PMID: 30097089.
      View in: PubMed
    2. 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 Res. 2018 Jan 04; 46(D1):D618-D623. PMID: 29106569.
      View in: PubMed
    3. Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC. A global view of structure-function relationships in the tautomerase superfamily. J Biol Chem. 2018 Feb 16; 293(7):2342-2357. PMID: 29184004.
      View in: PubMed
    4. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 01 01; 2017. PMID: 28605775.
      View in: PubMed
    5. Holliday GL, Davidson R, Akiva E, Babbitt PC. Evaluating Functional Annotations of Enzymes Using the Gene Ontology. Methods Mol Biol. 2017; 1446:111-132. PMID: 27812939.
      View in: PubMed
    6. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017(1). PMID: 28365730.
      View in: PubMed
    7. 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, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 04; 45(D1):D190-D199. PMID: 27899635.
      View in: PubMed
    8. 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. 2016 07 01; 32(13):2065-6. PMID: 27153692; PMCID: PMC4920114.
    9. 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, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database (Oxford). 2015; 2015:bav063. PMID: 26284514; PMCID: PMC4499208.
    10. 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 (Oxford). 2015; 2015:bav043. PMID: 25957950; PMCID: PMC4425939.
    11. 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, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015 Jun; 83(6):1005-13. PMID: 25820941.
      View in: PubMed
    12. 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. 2015 Mar 10; 54(9):1807-18. PMID: 25654171; PMCID: PMC4839199.
    13. Holliday GL, Rahman SA, Furnham N, Thornton JM. Exploring the biological and chemical complexity of the ligases. J Mol Biol. 2014 May 15; 426(10):2098-111. PMID: 24657765; PMCID: PMC4018984.
    14. Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM. EC-BLAST: a tool to automatically search and compare enzyme reactions. Nat Methods. 2014 Feb; 11(2):171-4. PMID: 24412978.
      View in: PubMed
    15. 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 Res. 2014 Jan; 42(Database issue):D485-9. PMID: 24319146; PMCID: PMC3964973.
    16. 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, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. PMID: 24271399; PMCID: PMC3965090.
    17. 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. The EBI enzyme portal. Nucleic Acids Res. 2013 Jan; 41(Database issue):D773-80. PMID: 23175605.
      View in: PubMed
    18. 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 Comput Biol. 2012; 8(3):e1002403. PMID: 22396634; PMCID: PMC3291543.
    19. Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D783-9. PMID: 22058127; PMCID: PMC3244993.
    20. 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 Res. 2012 Jan; 40(Database issue):D776-82. PMID: 22006843; PMCID: PMC3245072.
    21. 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. FEBS J. 2011 Oct; 278(20):3835-45. PMID: 21605342; PMCID: PMC3258480.
    22. Fischer JD, Holliday GL, Rahman SA, Thornton JM. The structures and physicochemical properties of organic cofactors in biocatalysis. J Mol Biol. 2010 Nov 12; 403(5):803-24. PMID: 20850456.
      View in: PubMed
    23. Fischer JD, Holliday GL, Thornton JM. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics. 2010 Oct 01; 26(19):2496-7. PMID: 20679331; PMCID: PMC2944199.
    24. Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Small Molecule Subgraph Detector (SMSD) toolkit. J Cheminform. 2009 Aug 10; 1(1):12. PMID: 20298518; PMCID: PMC2820491.
    25. Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol. 2009 Jul 17; 390(3):560-77. PMID: 19447117.
      View in: PubMed
    26. Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics. 2009 Aug 15; 25(16):2088-9. PMID: 19369503.
      View in: PubMed
    27. Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem. 2008 Nov; 13(8):1205-18. PMID: 18604568.
      View in: PubMed
    28. 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. Nat Prod Rep. 2007 Oct; 24(5):972-87. PMID: 17898893.
      View in: PubMed
    29. Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. The chemistry of protein catalysis. J Mol Biol. 2007 Oct 05; 372(5):1261-77. PMID: 17727879.
      View in: PubMed
    30. Torrance JW, Holliday GL, Mitchell JB, Thornton JM. The geometry of interactions between catalytic residues and their substrates. J Mol Biol. 2007 Jun 15; 369(4):1140-52. PMID: 17466330.
      View in: PubMed
    31. O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. Using reaction mechanism to measure enzyme similarity. J Mol Biol. 2007 May 18; 368(5):1484-99. PMID: 17400244; PMCID: PMC3461574.
    32. 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 Res. 2007 Jan; 35(Database issue):D515-20. PMID: 17082206; PMCID: PMC1634735.
    33. Holliday GL, Murray-Rust P, Rzepa HS. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. J Chem Inf Model. 2006 Jan-Feb; 46(1):145-57. PMID: 16426051.
      View in: PubMed
    34. Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. MACiE: a database of enzyme reaction mechanisms. Bioinformatics. 2005 Dec 01; 21(23):4315-6. PMID: 16188925; PMCID: PMC2748267.
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