Research Topics
| Patricia BabbittSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
A gold standard set of mechanistically diverse enzyme superfamiliesShoshana D Brown
Department of Biopharmaceutical Sciences, University of California, 1700 4th Street, San Francisco, San Francisco, CA 94143-2550, USA
Genome Biol 7:R8. 2006..The gold standard set represents four fold classes and differing clustering difficulties, and includes five superfamilies, 91 families, 4,887 sequences and 282 structures...- Comparison of methods for genomic localization of gene trap sequencesCourtney A Harper
Department of Biopharmaceutical Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94143 2250, USA
BMC Genomics 7:236. 2006..Known genome coordinates for the cognate set of full-length genes (1,659 sequences) were used to evaluate localization results... 
Definitions of enzyme function for the structural genomics eraPatricia C Babbitt
Department of Biopharmaceutical Sciences, University of California, 513 Parnassus Street, San Francisco, CA 94143 0446, USA
Curr Opin Chem Biol 7:230-7. 2003..A new approach to describing enzyme function has been proposed that might improve our capabilities for functional inference for members of enzyme superfamilies...- Using the Structure-function Linkage Database to characterize functional domains in enzymesShoshana Brown
University of California, San Francisco, San Francisco, California, USA
Curr Protoc Bioinformatics . 2006..It is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases... - Intersect: identification and visualization of overlaps in database search resultsScott C-H Pegg
Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
Bioinformatics 19:1997-9. 2003..AVAILABILITY: The Intersect program is available from the Babbitt laboratory website at http://www.babbittlab.ucsf.edu/software/intersect.. - structureViz: linking Cytoscape and UCSF ChimeraJohn H Morris
Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
Bioinformatics 23:2345-7. 2007..This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains and residues, mostly through the use of context menus... - Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamilyMargaret E Glasner
Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
J Mol Biol 360:228-50. 2006..Finally, a combination of evolutionary, structural, and sequence analyses identified characteristics that might prime proteins, such as Amycolatopsis OSBS/NAAAR, for the evolution of new activities... - Evolution of enzyme superfamiliesMargaret E Glasner
Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
Curr Opin Chem Biol 10:492-7. 2006..Understanding how enzyme superfamilies evolve is vital for accurate genome annotation, predicting protein functions, and protein engineering... - Prediction and assignment of function for a divergent N-succinyl amino acid racemaseLing Song
Department of Biochemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
Nat Chem Biol 3:486-91. 2007..These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested... - Evolution of function in the "two dinucleotide binding domains" flavoproteinsSunil Ojha
Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, USA
PLoS Comput Biol 3:e121. 2007..Overlaid on this foundation of conserved interactions, nature has conscripted different protein partners to serve as electron acceptors, thereby generating diversification of function across the superfamily... - Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage databaseScott C-H Pegg
Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2250, USA
Biochemistry 45:2545-55. 2006..The SFLD is freely accessible at http://sfld.rbvi.ucsf.edu... - D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamilyJulie Akana
Department of Biochemistry, University of Illinois at Urbana Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, USA
Biochemistry 45:2493-503. 2006..Instead, this "superfamily" may result from assembly from smaller modules, including the conserved phosphate binding motif associated with the C-terminal (beta/alpha)(2)-quarter barrel... - Automated discovery of 3D motifs for protein function annotationBenjamin J Polacco
Department of Biopharmaceutical Sciences, University of California, San Francisco, 94143-2250, USA
Bioinformatics 22:723-30. 2006..AVAILABILITY: Source code is freely available for academic use by contacting the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online... - The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouseAlex S Nord
University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA
Nucleic Acids Res 34:D642-8. 2006.... - Divergent evolution in the enolase superfamily: the interplay of mechanism and specificityJohn A Gerlt
Departments of Biochemistry and Chemistry, University of Illinois, Urbana, IL 61801, USA
Arch Biochem Biophys 433:59-70. 2005..In this minireview, our current understanding of structure/function relationships in the divergent members of the superfamily is reviewed, and the use of this knowledge for our future studies is proposed... - Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestorShelley D Copley
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
Biochemistry 43:13981-95. 2004.... - Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinaseWalter R P Novak
Department of Biopharmaceutical Sciences, University of California, 600 16 Street, San Francisco, California 94143, USA
Biochemistry 43:13766-74. 2004..This study enhances our understanding of how the active sites of phosphagen kinases have evolved to recognize their respective substrates and catalyze their reactions... - Superfamily active site templatesElaine C Meng
Department of Pharmaceutical Chemistry, University of California, Genentech Hall, 600 Sixteenth Street, San Francisco, CA 94143-2240, USA
Proteins 55:962-76. 2004.... - The Structure Superposition DatabaseRanyee A Chiang
Department of Biopharmaceutical Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
Nucleic Acids Res 31:505-10. 2003..Features of the user interface module facilitate viewing multiple superpositions together. The SSD interface module can be downloaded from http://ssd.rbvi.ucsf.edu... - BayGenomics: a resource of insertional mutations in mouse embryonic stem cellsDoug Stryke
Department of Pharmaceutical Chemistry, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
Nucleic Acids Res 31:278-81. 2003..They can then obtain the mutant ES cell line for the purpose of generating knockout mice...
Research Grants
- BMI Bioinformatics Training GrantPatricia Babbitt; Fiscal Year: 2007..abstract_text> ..
- LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGYPatricia Babbitt; Fiscal Year: 2004..abstract_text> ..
- LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGYPatricia Babbitt; Fiscal Year: 2009..These studies will focus first on superfamilies that use FAD cofactors. ..