Babbitt PC - Search Results

1

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. Almonacid DE, et al. Among authors: babbitt pc. PLoS Comput Biol. 2010 Mar 12;6(3):e1000700. doi: 10.1371/journal.pcbi.1000700. PLoS Comput Biol. 2010. PMID: 20300652 Free PMC article.

2

Toward mechanistic classification of enzyme functions.

Almonacid DE, Babbitt PC. Almonacid DE, et al. Among authors: babbitt pc. 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.

3

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: babbitt pc. 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.

4

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.

Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. Wallrapp FH, et al. Among authors: babbitt pc. Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1196-202. doi: 10.1073/pnas.1300632110. Epub 2013 Mar 14. Proc Natl Acad Sci U S A. 2013. PMID: 23493556 Free PMC article.

5

Evolution of enzyme superfamilies.

Glasner ME, Gerlt JA, Babbitt PC. Glasner ME, et al. Among authors: babbitt pc. Curr Opin Chem Biol. 2006 Oct;10(5):492-7. doi: 10.1016/j.cbpa.2006.08.012. Epub 2006 Aug 28. Curr Opin Chem Biol. 2006. PMID: 16935022 Review.

6

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

Chiang RA, Sali A, Babbitt PC. Chiang RA, et al. Among authors: babbitt pc. PLoS Comput Biol. 2008 Aug 1;4(8):e1000142. doi: 10.1371/journal.pcbi.1000142. PLoS Comput Biol. 2008. PMID: 18670595 Free PMC article.

7

An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations.

Atkinson HJ, Babbitt PC. Atkinson HJ, et al. Among authors: babbitt pc. PLoS Comput Biol. 2009 Oct;5(10):e1000541. doi: 10.1371/journal.pcbi.1000541. Epub 2009 Oct 23. PLoS Comput Biol. 2009. PMID: 19851441 Free PMC article.

8

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Schnoes AM, et al. Among authors: babbitt pc. PLoS Comput Biol. 2009 Dec;5(12):e1000605. doi: 10.1371/journal.pcbi.1000605. Epub 2009 Dec 11. PLoS Comput Biol. 2009. PMID: 20011109 Free PMC article.

9

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

Holliday GL, Brown SD, Mischel D, Polacco BJ, Babbitt PC. Holliday GL, et al. Among authors: babbitt pc. Database (Oxford). 2020 Jan 1;2020:baaa034. doi: 10.1093/database/baaa034. Database (Oxford). 2020. PMID: 32449511 Free PMC article.

10

Evolution of function in the "two dinucleotide binding domains" flavoproteins.

Ojha S, Meng EC, Babbitt PC. Ojha S, et al. Among authors: babbitt pc. PLoS Comput Biol. 2007 Jul;3(7):e121. doi: 10.1371/journal.pcbi.0030121. PLoS Comput Biol. 2007. PMID: 17658942 Free PMC article.

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