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    Gemma Holliday, PhD

    TitleAssistant Researcher
    SchoolUCSF School of Pharmacy
    DepartmentBioengineering
    Address1700 4th Street
    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. 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 Jul 1; 32(13):2065-6. PMID: 27153692.
        View in: PubMed
      2. 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.
      3. 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.
      4. 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; PMCID: PMC4446195.
      5. 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.
        View in: PubMed
      6. Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol. 2014 Oct; 10(10):e1003874. PMID: 25299649; PMCID: PMC4191879.
      7. 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.
      8. 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; PMCID: PMC4122987.
      9. 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.
      10. 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.
      11. 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; PMCID: PMC3531056.
      12. 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.
      13. 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.
      14. 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.
      15. 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.
      16. 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
      17. Fischer JD, Holliday GL, Thornton JM. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics. 2010 Oct 1; 26(19):2496-7. PMID: 20679331; PMCID: PMC2944199.
      18. Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Small Molecule Subgraph Detector (SMSD) toolkit. J Cheminform. 2009; 1(1):12. PMID: 20298518; PMCID: PMC2820491.
      19. 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
      20. 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
      21. 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
      22. 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
      23. Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. The chemistry of protein catalysis. J Mol Biol. 2007 Oct 5; 372(5):1261-77. PMID: 17727879.
        View in: PubMed
      24. 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
      25. 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.
      26. 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.
      27. 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
      28. 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 1; 21(23):4315-6. PMID: 16188925; PMCID: PMC2748267.
      29. Gemma L. Holliday, John B. O. Mitchell, Peter Murray-Rust. . CMLSnap: Animated reaction mechanisms. INTERNET JOURNAL OF CHEMISTRY. 2004; 7(4).
      30. Matthew L. Clarke, Gemma L. Holliday, Alexandra M. Z. Slawin, J. Derek Woollins. . Highly electron rich alkyl- and dialkyl-N-pyrrolidinyl phosphines: an evaluation of their electronic and structural properties. JOURNAL OF THE CHEMICAL SOCIETY-DALTON TRANSACTIONS. 2002; (6):1093-1103.
      31. Matthew L. Clarke, Gemma L. Holliday, Alexandra M. Z. Slawin, J. Derek Woollins. . First examples of M-Se-P-N-N heterocycles. INORGANIC CHEMISTRY COMMUNICATIONS. 2001; 4(3):115-118.
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