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MACiE: a database of enzyme reaction mechanisms.
Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. Holliday GL, et al. Among authors: almonacid de. Bioinformatics. 2005 Dec 1;21(23):4315-6. doi: 10.1093/bioinformatics/bti693. Epub 2005 Sep 27. Bioinformatics. 2005. PMID: 16188925 Free PMC article.
Using reaction mechanism to measure enzyme similarity.
O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. O'Boyle NM, et al. Among authors: almonacid de. J Mol Biol. 2007 May 18;368(5):1484-99. doi: 10.1016/j.jmb.2007.02.065. Epub 2007 Mar 2. J Mol Biol. 2007. PMID: 17400244 Free PMC article.
The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. Holliday GL, et al. Among authors: almonacid de. J Mol Biol. 2007 Oct 5;372(5):1261-77. doi: 10.1016/j.jmb.2007.07.034. Epub 2007 Aug 2. J Mol Biol. 2007. PMID: 17727879
MACiE: exploring the diversity of biochemical reactions.
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. Holliday GL, et al. Among authors: almonacid de. Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. doi: 10.1093/nar/gkr799. Epub 2011 Nov 3. Nucleic Acids Res. 2012. PMID: 22058127 Free PMC article.
The Structure-Function Linkage Database.
Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. Akiva E, et al. Among authors: almonacid de. Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23. Nucleic Acids Res. 2014. PMID: 24271399 Free PMC article.
Toward mechanistic classification of enzyme functions.
Almonacid DE, Babbitt PC. Almonacid DE, et al. Curr Opin Chem Biol. 2011 Jun;15(3):435-42. doi: 10.1016/j.cbpa.2011.03.008. Epub 2011 Apr 12. Curr Opin Chem Biol. 2011. PMID: 21489855 Free PMC article. Review.
26 results