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Items: 1 to 20 of 95


The Enzyme Function Initiative.

Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV.

Biochemistry. 2011 Nov 22;50(46):9950-62. doi: 10.1021/bi201312u. Epub 2011 Oct 26. Review.


Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.

Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL.

Biochim Biophys Acta. 2015 Aug;1854(8):1019-37. doi: 10.1016/j.bbapap.2015.04.015. Epub 2015 Apr 18. Review.


Discovery of new enzymes and metabolic pathways by using structure and genome context.

Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP.

Nature. 2013 Oct 31;502(7473):698-702. doi: 10.1038/nature12576. Epub 2013 Sep 22.


Inference of functional properties from large-scale analysis of enzyme superfamilies.

Brown SD, Babbitt PC.

J Biol Chem. 2012 Jan 2;287(1):35-42. doi: 10.1074/jbc.R111.283408. Epub 2011 Nov 8. Review.


Bioinformatic and enzymatic characterization of the MAPEG superfamily.

Bresell A, Weinander R, Lundqvist G, Raza H, Shimoji M, Sun TH, Balk L, Wiklund R, Eriksson J, Jansson C, Persson B, Jakobsson PJ, Morgenstern R.

FEBS J. 2005 Apr;272(7):1688-703.


Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.

Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A.

J Struct Funct Genomics. 2009 Apr;10(2):107-25. doi: 10.1007/s10969-008-9056-5. Epub 2009 Feb 14.


Biochemical functional predictions for protein structures of unknown or uncertain function.

Mills CL, Beuning PJ, Ondrechen MJ.

Comput Struct Biotechnol J. 2015 Feb 18;13:182-91. doi: 10.1016/j.csbj.2015.02.003. eCollection 2015. Review.


Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC.

Pac Symp Biocomput. 2005:358-69.


Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.

Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.

Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. doi: 10.1073/pnas.1112081109. Epub 2012 Mar 5.


Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

Chiang RA, Sali A, Babbitt PC.

PLoS Comput Biol. 2008 Aug 1;4(8):e1000142. doi: 10.1371/journal.pcbi.1000142.


Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.

Nagao C, Nagano N, Mizuguchi K.

PLoS One. 2014 Jan 8;9(1):e84623. doi: 10.1371/journal.pone.0084623. eCollection 2014.


Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O.

BMC Bioinformatics. 2008 Jan 11;9:17. doi: 10.1186/1471-2105-9-17.


Thematic minireview series on enzyme evolution in the post-genomic era.

Allewell NM.

J Biol Chem. 2012 Jan 2;287(1):1-2. doi: 10.1074/jbc.R111.307322. Epub 2011 Nov 8.


Evolution of function in protein superfamilies, from a structural perspective.

Todd AE, Orengo CA, Thornton JM.

J Mol Biol. 2001 Apr 6;307(4):1113-43.


Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.

Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP.

Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275.


Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .

Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA.

Biochemistry. 2009 Dec 8;48(48):11546-58. doi: 10.1021/bi901731c.


Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.

Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC.

Biochemistry. 2006 Feb 28;45(8):2545-55.


Sequence- and activity-based screening of microbial genomes for novel dehalogenases.

Chan WY, Wong M, Guthrie J, Savchenko AV, Yakunin AF, Pai EF, Edwards EA.

Microb Biotechnol. 2010 Jan;3(1):107-20. doi: 10.1111/j.1751-7915.2009.00155.x. Epub 2009 Nov 12.


Evolution of enzyme superfamilies.

Glasner ME, Gerlt JA, Babbitt PC.

Curr Opin Chem Biol. 2006 Oct;10(5):492-7. Epub 2006 Aug 28. Review.

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