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Patricia Babbitt
Patricia Babbitt
Professor
Verified email at cgl.ucsf.edu
Title
Cited by
Cited by
Year
InterPro in 2017—beyond protein family and domain annotations
RD Finn, TK Attwood, PC Babbitt, A Bateman, P Bork, AJ Bridge, ...
Nucleic acids research 45 (D1), D190-D199, 2017
15722017
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
AL Mitchell, TK Attwood, PC Babbitt, M Blum, P Bork, A Bridge, SD Brown, ...
Nucleic acids research 47 (D1), D351-D360, 2019
15172019
A large-scale evaluation of computational protein function prediction
P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ...
Nature methods 10 (3), 221-227, 2013
10882013
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
AM Schnoes, SD Brown, I Dodevski, PC Babbitt
PLoS computational biology 5 (12), e1000605, 2009
8202009
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies
JA Gerlt, PC Babbitt
Annual review of biochemistry 70 (1), 209-246, 2001
6602001
Encyclopedia of computational chemistry
PR Schleyer
(No Title), 1998
5961998
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
HJ Atkinson, JH Morris, TE Ferrin, PC Babbitt
PloS one 4 (2), e4345, 2009
4842009
The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the α-protons of carboxylic acids
PC Babbitt, MS Hasson, JE Wedekind, DRJ Palmer, WC Barrett, GH Reed, ...
Biochemistry 35 (51), 16489-16501, 1996
4291996
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17, 1-19, 2016
4252016
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome biology 20, 1-23, 2019
3882019
Understanding enzyme superfamilies: chemistry as the fundamental determinant in the evolution of new catalytic activities
PC Babbitt, JA Gerlt
Journal of Biological Chemistry 272 (49), 30591-30594, 1997
3671997
Evolution of enzyme superfamilies
ME Glasner, JA Gerlt, PC Babbitt
Current opinion in chemical biology 10 (5), 492-497, 2006
2872006
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells
D Stryke, M Kawamoto, CC Huang, SJ Johns, LA King, CA Harper, ...
Nucleic Acids Research 31 (1), 278-281, 2003
2822003
Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl: adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA …
PC Babbitt, GL Kenyon, BM Martin, H Charest, M Slyvestre, JD Scholten, ...
Biochemistry 31 (24), 5594-5604, 1992
2761992
The structure–function linkage database
E Akiva, S Brown, DE Almonacid, AE Barber 2nd, AF Custer, MA Hicks, ...
Nucleic acids research 42 (D1), D521-D530, 2014
2582014
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity
JA Gerlt, PC Babbitt, I Rayment
Archives of biochemistry and biophysics 433 (1), 59-70, 2005
2462005
Evolutionary potential of (β/α) 8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily
DMZ Schmidt, EC Mundorff, M Dojka, E Bermudez, JE Ness, ...
Biochemistry 42 (28), 8387-8393, 2003
2292003
Can sequence determine function?
JA Gerlt, PC Babbitt
Genome biology 1, 1-10, 2000
2252000
Glutathione transferases are structural and functional outliers in the thioredoxin fold
HJ Atkinson, PC Babbitt
Biochemistry 48 (46), 11108-11116, 2009
2022009
Leveraging enzyme structure− function relationships for functional inference and experimental design: the structure− function linkage database
SCH Pegg, SD Brown, S Ojha, J Seffernick, EC Meng, JH Morris, ...
Biochemistry 45 (8), 2545-2555, 2006
1992006
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