Gemma L. Holliday

Publication Activity (10 Years)

Years Active: 2005-2020
Publications (10 Years): 6

Top Topics

Chemical Reaction

Protein Families

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

PLoS Comput. Biol.

Publications

Gemma L. Holliday, Shoshana D. Brown, David Mischel, Benjamin J. Polacco, Patricia C. Babbitt
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database J. Biol. Databases Curation 2020 (2020)
António J. M. Ribeiro, Gemma L. Holliday, Nicholas Furnham, Jonathan D. Tyzack, Katherine Ferris, Janet M. Thornton
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Res. 46 (Database-Issue) (2018)
Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017 (2017)
Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017 (2017)
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45 (Database-Issue) (2017)
Syed Asad Rahman, Gilliean Torrance, Lorenzo Baldacci, Sergio Martínez Cuesta, Franz Fenninger, Nimish Gopal, Saket Choudhary, John W. May, Gemma L. Holliday, Christoph Steinbeck, Janet M. Thornton
Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinform. 32 (13) (2016)
Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database J. Biol. Databases Curation 2015 (2015)
Frederic B. Bastian, Marcus C. Chibucos, Pascale Gaudet, Michelle G. Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra E. Orchard, Sylvain Poux, Nives Skunca, Marc Robinson-Rechavi
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database J. Biol. Databases Curation 2015 (2015)
Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach. PLoS Comput. Biol. 10 (10) (2014)
Eyal Akiva, Shoshana D. Brown, Daniel E. Almonacid, Alan E. Barber II, Ashley F. Custer, Michael A. Hicks, Conrad C. Huang, Florian Lauck, Susan T. Mashiyama, Elaine C. Meng, David Mischel, John H. Morris, Sunil Ojha, Alexandra M. Schnoes, Doug Stryke, Jeffrey M. Yunes, Thomas E. Ferrin, Gemma L. Holliday, Patricia C. Babbitt
The Structure-Function Linkage Database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Nicholas Furnham, Gemma L. Holliday, Tjaart A. P. de Beer, Julius O. B. Jacobsen, William R. Pearson, Janet M. Thornton
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 42 (Database-Issue) (2014)
Rafael Alcántara, Joseph Onwubiko, Hong Cao, Paula de Matos, Jennifer A. Cham, Julius O. B. Jacobsen, Gemma L. Holliday, Julia D. Fischer, Syed Asad Rahman, Bijay Jassal, Mickael Goujon, Francis Rowland, Sameer Velankar, Rodrigo Lopez, John P. Overington, Gerard J. Kleywegt, Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Janet M. Thornton, Christoph Steinbeck
The EBI enzyme portal. Nucleic Acids Res. 41 (Database-Issue) (2013)
Gemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson
MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res. 40 (Database-Issue) (2012)
Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies. PLoS Comput. Biol. 8 (3) (2012)
Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed Asad Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res. 40 (Database-Issue) (2012)
Julia D. Fischer, Gemma L. Holliday, Janet M. Thornton
The CoFactor database: organic cofactors in enzyme catalysis. Bioinform. 26 (19) (2010)
Claudia Andreini, Ivano Bertini, Gabriele Cavallaro, Gemma L. Holliday, Janet M. Thornton
Metal-MACiE: a database of metals involved in biological catalysis. Bioinform. 25 (16) (2009)
Syed Asad Rahman, Matthew Bashton, Gemma L. Holliday, Rainer Schrader, Janet M. Thornton
Small Molecule Subgraph Detector (SMSD) toolkit. J. Cheminformatics 1 (2009)
Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Noel M. O'Boyle, James W. Torrance, Peter Murray-Rust, John B. O. Mitchell, Janet M. Thornton
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res. 35 (Database-Issue) (2007)
Gemma L. Holliday, Peter Murray-Rust, Henry S. Rzepa
Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions. J. Chem. Inf. Model. 46 (1) (2006)
Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Noel M. O'Boyle, Peter Murray-Rust, Janet M. Thornton, John B. O. Mitchell
MACiE: a database of enzyme reaction mechanisms. Bioinform. 21 (23) (2005)