Gemma L Holliday

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc MACiE: exploring the diversity of biochemical reactions
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D783-9. 2012
  2. pmc Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Cambridge, UK
    FEBS J 278:3835-45. 2011
  3. ncbi request reprint Understanding the functional roles of amino acid residues in enzyme catalysis
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J Mol Biol 390:560-77. 2009
  4. ncbi request reprint Evolution of enzymes and pathways for the biosynthesis of cofactors
    Gemma L Holliday
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK CB10 1SD
    Nat Prod Rep 24:972-87. 2007
  5. ncbi request reprint The chemistry of protein catalysis
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 372:1261-77. 2007
  6. pmc MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 35:D515-20. 2007
  7. pmc MACiE: a database of enzyme reaction mechanisms
    Gemma L Holliday
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK
    Bioinformatics 21:4315-6. 2005
  8. ncbi request reprint The geometry of interactions between catalytic residues and their substrates
    James W Torrance
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    J Mol Biol 369:1140-52. 2007
  9. doi request reprint EC-BLAST: a tool to automatically search and compare enzyme reactions
    Syed Asad Rahman
    European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    Nat Methods 11:171-4. 2014
  10. pmc Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies
    Nicholas Furnham
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 8:e1002403. 2012

Collaborators

Detail Information

Publications17

  1. pmc MACiE: exploring the diversity of biochemical reactions
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D783-9. 2012
    ..We present new tools for exploring the data in MACiE and comparing entries as well as new analyses of the data and new searches, many of which can now be accessed via dedicated Perl scripts...
  2. pmc Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Cambridge, UK
    FEBS J 278:3835-45. 2011
    ..This work highlights how the enzymes that we see today reflect millions of years of evolution, involving de novo design followed by exquisite regulation and modulation to create optimal fitness for life...
  3. ncbi request reprint Understanding the functional roles of amino acid residues in enzyme catalysis
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J Mol Biol 390:560-77. 2009
    ....
  4. ncbi request reprint Evolution of enzymes and pathways for the biosynthesis of cofactors
    Gemma L Holliday
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK CB10 1SD
    Nat Prod Rep 24:972-87. 2007
    ..Retrograde and patchwork models are highlighted and their relevance to our knowledge of pathway processes and enzymes is examined. Pathway complexity is explained in terms of the acquisition of broad specificity enzymes...
  5. ncbi request reprint The chemistry of protein catalysis
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 372:1261-77. 2007
    ..The analysis presented provides a better understanding of the mechanisms of enzyme catalysis and may act as an initial step in the validation and prediction of mechanism in an enzyme active site...
  6. pmc MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 35:D515-20. 2007
    ..We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/..
  7. pmc MACiE: a database of enzyme reaction mechanisms
    Gemma L Holliday
    Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge Lensfield Road, Cambridge, CB2 1EW, UK
    Bioinformatics 21:4315-6. 2005
    ....
  8. ncbi request reprint The geometry of interactions between catalytic residues and their substrates
    James W Torrance
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    J Mol Biol 369:1140-52. 2007
    ..Such statistics provide limits on "expected geometries" for catalytic residues, which will help to identify these residues and elucidate enzyme mechanisms...
  9. doi request reprint EC-BLAST: a tool to automatically search and compare enzyme reactions
    Syed Asad Rahman
    European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    Nat Methods 11:171-4. 2014
    ..EC-BLAST has the potential to improve enzyme classification, identify previously uncharacterized or new biochemical transformations, improve the assignment of enzyme function to sequences, and assist in enzyme engineering. ..
  10. pmc Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies
    Nicholas Furnham
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 8:e1002403. 2012
    ..This reinforces the hypothesis that relatively few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life...
  11. doi request reprint The structures and physicochemical properties of organic cofactors in biocatalysis
    Julia D Fischer
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J Mol Biol 403:803-24. 2010
    ..Finally, we show that the molecular functions of the cofactors not only may duplicate reactions performed by inorganic metal cofactors and amino acids, the cell's other catalytic tools, but also provide novel chemistries for catalysis...
  12. pmc The CoFactor database: organic cofactors in enzyme catalysis
    Julia D Fischer
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 26:2496-7. 2010
    ..Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database...
  13. ncbi request reprint The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes
    Nicholas Furnham
    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
    Nucleic Acids Res 42:D485-9. 2014
    ..The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface. ..
  14. pmc The EBI enzyme portal
    Rafael Alcántara
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 41:D773-80. 2013
    ..The fact that these data reside in separate databases makes information discovery cumbersome. The main goal of the portal is to simplify this process for end users...
  15. ncbi request reprint Exploring the biological and chemical complexity of the ligases
    Gemma L Holliday
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Electronic address
    J Mol Biol 426:2098-111. 2014
    ..However, a common theme is that a single conserved domain (often the nucleoside triphosphate binding domain) is combined with ancillary domains that provide the variation in substrate binding and function. ..
  16. pmc FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies
    Nicholas Furnham
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D776-82. 2012
    ..The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree...
  17. pmc Small Molecule Subgraph Detector (SMSD) toolkit
    Syed Asad Rahman
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    J Cheminform 1:12. 2009
    ..We also propose a novel method by which solutions obtained by each MCS run can be ranked using chemical filters such as stereochemistry, bond energy, etc...