Analyzing sex imbalance in EGA and dbGaP biological databases: Recommendations for better practices

Authors: Ruiz-Serra, Victoria ^{1, 2, 9}, Buslón, Nataly ^{3, 9, ∗}, Philippe, Olivier R. ¹, Saby, Diego ⁴, Morales, María ¹, Pontes, Camila ¹, Andirkó, Alejandro Muñoz ⁵, Holliday, Gemma L. ⁶, Jené, Aina ⁷, Moldes, Mauricio ⁷, Rambla, Jordi ⁷, Valencia, Alfonso ^{1, 8}, Rementeria, María José ¹, Cortés, Atia ^{1, 9}, Cirillo, Davide ^{1, 9, 10, ∗∗}

Source: In iScience 18 October 2024 27(10)

Role of ammonia-lyases in the synthesis of the dithiomethylamine ligand during [FeFe]-hydrogenase maturation

Authors: Pagnier, Adrien, Balci, Batuhan, Shepard, Eric M., Yang, Hao, Drena, Alex, Holliday, Gemma L., Hoffman, Brian M., Broderick, William E., Broderick, Joan B.

Source: In Journal of Biological Chemistry October 2024 300(10)

A global analysis of function and conservation of catalytic residues in enzymes

Authors: Ribeiro, António J.M., Tyzack, Jonathan D., Borkakoti, Neera, Holliday, Gemma L., Thornton, Janet M.

Source: In Journal of Biological Chemistry 10 January 2020 295(2):314-324

A global view of structure–function relationships in the tautomerase superfamily

Alternate Title: Tautomerase superfamily structure–function relationships (English)

Authors: Davidson, Rebecca, Baas, Bert-Jan, Akiva, Eyal, Holliday, Gemma L., Polacco, Benjamin J., LeVieux, Jake A., Pullara, Collin R., Zhang, Yan Jessie, Whitman, Christian P., Babbitt, Patricia C. ^**

Source: In Journal of Biological Chemistry 16 February 2018 293(7):2342-2357

Evaluating Functional Annotations of Enzymes Using the Gene Ontology

Authors: Holliday, Gemma L., Davidson, Rebecca, Akiva, Eyal, Babbitt, Patricia C.

Source: Methods in molecular biology. 1446:111-132

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN609112190&indx=1&recIds=ETOCRN609112190

Exploring the Biological and Chemical Complexity of the Ligases

Authors: Holliday, Gemma L., Rahman, Syed Asad, Furnham, Nicholas, Thornton, Janet M.

Source: In Journal of Molecular Biology 15 May 2014 426(10):2098-2111

[FeFe]-Hydrogenase Maturation: Insights into the Role HydE Plays in Dithiomethylamine Biosynthesis

Authors: Betz, Jeremiah N., Boswell, Nicholas W., Fugate, Corey J., Holliday, Gemma L., Akiva, Eyal, Scott, Anna G., Babbitt, Patricia C., Peters, John W., Shepard, Eric M., Broderick, Joan B.

Source: Biochemistry. 54(9):1807-1818

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN600071930&indx=1&recIds=ETOCRN600071930

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

Authors: Holliday, Gemma L^1,2 (AUTHOR) gemma.l.holliday@gmail.com, Brown, Shoshana D¹ (AUTHOR), Mischel, David¹ (AUTHOR), Polacco, Benjamin J¹ (AUTHOR), Babbitt, Patricia C^1,3,4 (AUTHOR) gemma.l.holliday@gmail.com

Source: Database: The Journal of Biological Databases & Curation. 2020, Vol. 2020, p1-15. 15p.

Subject Terms: *ENZYMES, *AMINO acid sequence, *PROTEIN structure, *GROSS motor ability, *CLASSIFICATION, *ENOLASE

The Structures and Physicochemical Properties of Organic Cofactors in Biocatalysis

Authors: Fischer, Julia D., Holliday, Gemma L., Rahman, Syed A., Thornton, Janet M.

Source: In Journal of Molecular Biology 12 November 2010 403(5):803-824

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

Authors: Holliday, Gemma L., Mitchell, John B.O., Thornton, Janet M.

Source: In Journal of Molecular Biology 2009 390(3):560-577

The Chemistry of Protein Catalysis

Authors: Holliday, Gemma L. ^†, Almonacid, Daniel E. ^†, Mitchell, John B.O., Thornton, Janet M.

Source: In Journal of Molecular Biology 2007 372(5):1261-1277

The Geometry of Interactions between Catalytic Residues and their Substrates

Authors: Torrance, James W., Holliday, Gemma L., Mitchell, John B.O., Thornton, Janet M.

Source: In Journal of Molecular Biology 2007 369(4):1140-1152

Using Reaction Mechanism to Measure Enzyme Similarity

Authors: O'Boyle, Noel M., Holliday, Gemma L., Almonacid, Daniel E., Mitchell, John B.O.

Source: In Journal of Molecular Biology 2007 368(5):1484-1499

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

Authors: Holliday, Gemma L.¹ gemma.l.holliday@gmail.com, Brown, Shoshana D.¹, Akiva, Eyal¹, Mischel, David¹, Hicks, Michael A.^1,2, Morris, John H.³, Huang, Conrad C.³, Meng, Elaine C.³, Pegg, Scott C.-H.⁴, Ferrin, Thomas E.^3,5, Babbitt, Patricia C.^1,3,5 babbitt@cgl.ucsf.edu

Source: Database: The Journal of Biological Databases & Curation. 2017, Vol. 2017 Issue 1, p1-12. 12p.

Subject Terms: *DATABASES, *MOLECULAR genetics, *ONTOLOGIES (Information retrieval), *CHEMICAL structure, *ENZYMES

Chapter One - Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Authors: Holliday, Gemma L. ^*, Akiva, Eyal ^*, Meng, Elaine C., Brown, Shoshana D. ^*, Calhoun, Sara ^*, Pieper, Ursula ^*, Sali, Andrej ^*, Booker, Squire J. ^**, Babbitt, Patricia C. ^*

Source: In Methods in Enzymology 2018 606:1-71

Small Molecule Subgraph Detector (SMSD) toolkit

Authors: Rahman Syed, Bashton Matthew, Holliday Gemma L, Schrader Rainer, Thornton Janet M

Source: Journal of Cheminformatics, Vol 1, Iss 1, p 12 (2009)

Subject Terms: Information technology, T58.5-58.64, Chemistry, QD1-999

File Description: electronic resource

Relation: http://www.jcheminf.com/content/1/1/12; https://doaj.org/toc/1758-2946

Access URL: https://doaj.org/article/6b26d1cd36e14376af9810bbf468c4c9

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.

Authors: Holliday, Gemma L.¹, Fischer, Julia D.¹, Mitchell, John B. O.², Thornton, Janet M.¹

Source: FEBS Journal. Oct2011, Vol. 278 Issue 20, p3835-3845. 11p.

Subject Terms: *AMINO acids, *PROTEIN structure, *ENZYME regulation, *CHEMICAL reactions, *BINDING sites, *COMPLEX compounds, *METAL ions

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