Gemma L Holliday

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi 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. ncbi 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
  3. ncbi 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
  4. ncbi 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 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
  6. ncbi 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
  7. ncbi 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 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. ncbi 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
  10. ncbi 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

Collaborators

Detail Information

Publications14

  1. ncbi 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. ncbi 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/..
  3. ncbi 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...
  4. ncbi 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 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
    ....
  6. ncbi 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...
  7. ncbi 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
    ..AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/...
  8. ncbi 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. ncbi 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...
  10. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...
  14. ncbi 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...