Gemma L. Holliday

According to our database, Gemma L. Holliday authored at least 20 papers between 2005 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2020

A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.

Gemma L. Holliday, Shoshana D. Brown, David Mischel, Benjamin J. Polacco, Patricia C. Babbitt

Database J. Biol. Databases Curation, 2020

2018

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

António J. M. Ribeiro, Gemma L. Holliday, Nicholas Furnham, Jonathan D. Tyzack, Katherine Ferris, Janet M. Thornton

Nucleic Acids Res., 2018

2017

InterPro in 2017 - beyond protein family and domain annotations.

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. 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, Young Mi 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

Nucleic Acids Res., 2017

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

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

Database J. Biol. Databases Curation, 2017

2016

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

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

Bioinform., 2016

2015

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

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

Database J. Biol. Databases Curation, 2015

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

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

Database J. Biol. Databases Curation, 2015

2014

Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach.

Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson

PLoS Comput. Biol., 2014

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Nicholas Furnham, Gemma L. Holliday, Tjaart A. P. de Beer, Julius O. B. Jacobsen, William R. Pearson, Janet M. Thornton

Nucleic Acids Res., 2014

The Structure-Function Linkage Database.

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

Nucleic Acids Res., 2014

2013

The EBI enzyme portal.

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

Nucleic Acids Res., 2013

2012

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies.

Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton

PLoS Comput. Biol., 2012

MACiE: exploring the diversity of biochemical reactions.

Gemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson

Nucleic Acids Res., 2012

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed Asad Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton

Nucleic Acids Res., 2012

2010

The CoFactor database: organic cofactors in enzyme catalysis.

Julia D. Fischer, Gemma L. Holliday, Janet M. Thornton

Bioinform., 2010

2009

Small Molecule Subgraph Detector (SMSD) toolkit.

Syed Asad Rahman, Matthew Bashton, Gemma L. Holliday, Rainer Schrader, Janet M. Thornton

J. Cheminformatics, 2009

Metal-MACiE: a database of metals involved in biological catalysis.

Claudia Andreini, Ivano Bertini, Gabriele Cavallaro, Gemma L. Holliday, Janet M. Thornton

Bioinform., 2009

2007

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

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

Nucleic Acids Res., 2007

2006

Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions.

Gemma L. Holliday, Peter Murray-Rust, Henry S. Rzepa

J. Chem. Inf. Model., 2006

2005

MACiE: a database of enzyme reaction mechanisms.

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Noel M. O'Boyle, Peter Murray-Rust, Janet M. Thornton, John B. O. Mitchell

Bioinform., 2005