| Year |
Citation |
Score |
| 2020 |
Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database : the Journal of Biological Databases and Curation. 2020. PMID 32449511 DOI: 10.1093/Database/Baaa034 |
0.528 |
|
| 2019 |
Ribeiro AJM, Tyzack JD, Borkakoti N, Holliday GL, Thornton JM. A global analysis of function and conservation of catalytic residues in enzymes. The Journal of Biological Chemistry. PMID 31796628 DOI: 10.1074/Jbc.Rev119.006289 |
0.744 |
|
| 2018 |
Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods in Enzymology. 606: 1-71. PMID 30097089 DOI: 10.1016/Bs.Mie.2018.06.004 |
0.424 |
|
| 2017 |
Davidson R, Baas BJ, Akiva E, Holliday GL, Polacco BJ, LeVieux JA, Pullara CR, Zhang YJ, Whitman CP, Babbitt PC. A global view of structure-function relationships in the tautomerase superfamily. The Journal of Biological Chemistry. PMID 29184004 DOI: 10.1074/Jbc.M117.815340 |
0.387 |
|
| 2017 |
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Research. PMID 29106569 DOI: 10.1093/Nar/Gkx1012 |
0.71 |
|
| 2017 |
Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database : the Journal of Biological Databases and Curation. 2017. PMID 28365730 DOI: 10.1093/Database/Bax006 |
0.398 |
|
| 2017 |
Holliday GL, Davidson R, Akiva E, Babbitt PC. Evaluating Functional Annotations of Enzymes Using the Gene Ontology. Methods in Molecular Biology (Clifton, N.J.). 1446: 111-132. PMID 27812939 DOI: 10.1007/978-1-4939-3743-1_9 |
0.345 |
|
| 2016 |
Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinformatics (Oxford, England). PMID 27153692 DOI: 10.1093/Bioinformatics/Btw096 |
0.644 |
|
| 2014 |
Holliday GL, Rahman SA, Furnham N, Thornton JM. Exploring the biological and chemical complexity of the ligases. Journal of Molecular Biology. 426: 2098-111. PMID 24657765 DOI: 10.1016/J.Jmb.2014.03.008 |
0.693 |
|
| 2014 |
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM. EC-BLAST: a tool to automatically search and compare enzyme reactions. Nature Methods. 11: 171-4. PMID 24412978 DOI: 10.1038/Nmeth.2803 |
0.756 |
|
| 2014 |
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Research. 42: D485-9. PMID 24319146 DOI: 10.1093/Nar/Gkt1243 |
0.73 |
|
| 2014 |
Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, ... ... Holliday GL, et al. The Structure-Function Linkage Database. Nucleic Acids Research. 42: D521-30. PMID 24271399 DOI: 10.1093/Nar/Gkt1130 |
0.753 |
|
| 2013 |
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, et al. The EBI enzyme portal. Nucleic Acids Research. 41: D773-80. PMID 23175605 DOI: 10.1093/Nar/Gks1112 |
0.718 |
|
| 2012 |
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM. Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. Plos Computational Biology. 8: e1002403. PMID 22396634 DOI: 10.1371/Journal.Pcbi.1002403 |
0.742 |
|
| 2012 |
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Research. 40: D783-9. PMID 22058127 DOI: 10.1093/Nar/Gkr799 |
0.809 |
|
| 2012 |
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM. FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Research. 40: D776-82. PMID 22006843 DOI: 10.1093/Nar/Gkr852 |
0.715 |
|
| 2011 |
Holliday GL, Fischer JD, Mitchell JB, Thornton JM. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. The Febs Journal. 278: 3835-45. PMID 21605342 DOI: 10.1111/J.1742-4658.2011.08190.X |
0.751 |
|
| 2010 |
Fischer JD, Holliday GL, Rahman SA, Thornton JM. The structures and physicochemical properties of organic cofactors in biocatalysis. Journal of Molecular Biology. 403: 803-24. PMID 20850456 DOI: 10.1016/J.Jmb.2010.09.018 |
0.654 |
|
| 2010 |
Fischer JD, Holliday GL, Thornton JM. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics (Oxford, England). 26: 2496-7. PMID 20679331 DOI: 10.1093/Bioinformatics/Btq442 |
0.736 |
|
| 2009 |
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Small Molecule Subgraph Detector (SMSD) toolkit. Journal of Cheminformatics. 1: 12. PMID 20298518 DOI: 10.1186/1758-2946-1-12 |
0.56 |
|
| 2009 |
Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. Journal of Molecular Biology. 390: 560-77. PMID 19447117 DOI: 10.1016/J.Jmb.2009.05.015 |
0.78 |
|
| 2009 |
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics (Oxford, England). 25: 2088-9. PMID 19369503 DOI: 10.1093/Bioinformatics/Btp256 |
0.594 |
|
| 2008 |
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 13: 1205-18. PMID 18604568 DOI: 10.1007/S00775-008-0404-5 |
0.594 |
|
| 2007 |
Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ. Evolution of enzymes and pathways for the biosynthesis of cofactors. Natural Product Reports. 24: 972-87. PMID 17898893 DOI: 10.1039/B703107F |
0.651 |
|
| 2007 |
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. The chemistry of protein catalysis. Journal of Molecular Biology. 372: 1261-77. PMID 17727879 DOI: 10.1016/J.Jmb.2007.07.034 |
0.827 |
|
| 2007 |
Torrance JW, Holliday GL, Mitchell JB, Thornton JM. The geometry of interactions between catalytic residues and their substrates. Journal of Molecular Biology. 369: 1140-52. PMID 17466330 DOI: 10.1016/J.Jmb.2007.03.055 |
0.744 |
|
| 2007 |
O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. Using reaction mechanism to measure enzyme similarity. Journal of Molecular Biology. 368: 1484-99. PMID 17400244 DOI: 10.1016/j.jmb.2007.02.065 |
0.79 |
|
| 2007 |
Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Research. 35: D515-20. PMID 17082206 DOI: 10.1093/Nar/Gkl774 |
0.787 |
|
| 2006 |
Holliday GL, Murray-Rust P, Rzepa HS. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. Journal of Chemical Information and Modeling. 46: 145-57. PMID 16426051 DOI: 10.1021/Ci0502698 |
0.335 |
|
| 2005 |
Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. MACiE: a database of enzyme reaction mechanisms. Bioinformatics (Oxford, England). 21: 4315-6. PMID 16188925 DOI: 10.1093/Bioinformatics/Bti693 |
0.792 |
|
| 2004 |
Holliday GL, Mitchell JBO, Murray-Rust P. CMLSnap: Animated reaction mechanisms Internet Journal of Chemistry. 7. |
0.353 |
|
| Show low-probability matches. |