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Items: 1 to 20 of 24


Using the structure-function linkage database to characterize functional domains in enzymes.

Brown S, Babbitt P.

Curr Protoc Bioinformatics. 2014 Dec 12;48:2.10.1-2.10.16. doi: 10.1002/0471250953.bi0210s48.


Reprogramming the chemodiversity of terpenoid cyclization by remolding the active site contour of epi-isozizaene synthase.

Li R, Chou WK, Himmelberger JA, Litwin KM, Harris GG, Cane DE, Christianson DW.

Biochemistry. 2014 Feb 25;53(7):1155-68. doi: 10.1021/bi401643u. Epub 2014 Feb 11.


Possible origin of life between mica sheets: does life imitate mica?

Hansma HG.

J Biomol Struct Dyn. 2013;31(8):888-95. doi: 10.1080/07391102.2012.718528. Epub 2012 Sep 11.


Toward mechanistic classification of enzyme functions.

Almonacid DE, Babbitt PC.

Curr Opin Chem Biol. 2011 Jun;15(3):435-42. doi: 10.1016/j.cbpa.2011.03.008. Epub 2011 Apr 12. Review.


A study on the flexibility of enzyme active sites.

Weng YZ, Chang DT, Huang YF, Lin CW.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S32. doi: 10.1186/1471-2105-12-S1-S32.


Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Almonacid DE, Yera ER, Mitchell JB, Babbitt PC.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000700. doi: 10.1371/journal.pcbi.1000700.


Structure of epi-isozizaene synthase from Streptomyces coelicolor A3(2), a platform for new terpenoid cyclization templates.

Aaron JA, Lin X, Cane DE, Christianson DW.

Biochemistry. 2010 Mar 2;49(8):1787-97. doi: 10.1021/bi902088z.


A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana.

Gunawardana D, Likic VA, Gayler KR.

Comp Funct Genomics. 2009:820381. doi: 10.1155/2009/820381. Epub 2009 Jul 2.


Exploring biosynthetic diversity with trichodiene synthase.

Vedula LS, Zhao Y, Coates RM, Koyama T, Cane DE, Christianson DW.

Arch Biochem Biophys. 2007 Oct 15;466(2):260-6. Epub 2007 Jun 28.


Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

Kensche PR, van Noort V, Dutilh BE, Huynen MA.

J R Soc Interface. 2008 Feb 6;5(19):151-70. Review.


A gold standard set of mechanistically diverse enzyme superfamilies.

Brown SD, Gerlt JA, Seffernick JL, Babbitt PC.

Genome Biol. 2006;7(1):R8. Epub 2006 Jan 31.


Metabolic interdependence of obligate intracellular bacteria and their insect hosts.

Zientz E, Dandekar T, Gross R.

Microbiol Mol Biol Rev. 2004 Dec;68(4):745-70. Review.


Network analysis of metabolic enzyme evolution in Escherichia coli.

Light S, Kraulis P.

BMC Bioinformatics. 2004 Feb 18;5:15.


Finding evolutionary relations beyond superfamilies: fold-based superfamilies.

Matsuda K, Nishioka T, Kinoshita K, Kawabata T, Go N.

Protein Sci. 2003 Oct;12(10):2239-51.


Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.

McLeish MJ, Kneen MM, Gopalakrishna KN, Koo CW, Babbitt PC, Gerlt JA, Kenyon GL.

J Bacteriol. 2003 Apr;185(8):2451-6.


A functional homolog of a yeast tRNA splicing enzyme is conserved in higher eukaryotes and in Escherichia coli.

Spinelli SL, Malik HS, Consaul SA, Phizicky EM.

Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14136-41.


Assembly of an active enzyme by the linkage of two protein modules.

Nixon AE, Warren MS, Benkovic SJ.

Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1069-73.


3-Carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: an alternate cycloisomerase motif.

Mazur P, Henzel WJ, Mattoo S, Kozarich JW.

J Bacteriol. 1994 Mar;176(6):1718-28.

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