Patricia Babbitt

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc A gold standard set of mechanistically diverse enzyme superfamilies
    Shoshana 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
  2. pmc Comparison of methods for genomic localization of gene trap sequences
    Courtney 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
  3. ncbi request reprint Definitions of enzyme function for the structural genomics era
    Patricia 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
  4. doi request reprint Using the Structure-function Linkage Database to characterize functional domains in enzymes
    Shoshana Brown
    University of California, San Francisco, San Francisco, California, USA
    Curr Protoc Bioinformatics . 2006
  5. ncbi request reprint Intersect: identification and visualization of overlaps in database search results
    Scott C H Pegg
    Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
    Bioinformatics 19:1997-9. 2003
  6. ncbi request reprint structureViz: linking Cytoscape and UCSF Chimera
    John H Morris
    Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
    Bioinformatics 23:2345-7. 2007
  7. ncbi request reprint Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily
    Margaret E Glasner
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    J Mol Biol 360:228-50. 2006
  8. ncbi request reprint Evolution of enzyme superfamilies
    Margaret E Glasner
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Curr Opin Chem Biol 10:492-7. 2006
  9. ncbi request reprint Prediction and assignment of function for a divergent N-succinyl amino acid racemase
    Ling 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
  10. pmc Evolution of function in the "two dinucleotide binding domains" flavoproteins
    Sunil Ojha
    Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, California, USA
    PLoS Comput Biol 3:e121. 2007

Research Grants

  1. BMI Bioinformatics Training Grant
    Patricia Babbitt; Fiscal Year: 2007
  2. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2004
  3. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2009

Collaborators

  • JOHN GERLT
  • Elaine C Meng
  • Matthew P Jacobson
  • Conrad C Huang
  • Thomas E Ferrin
  • Margaret E Glasner
  • Walter R P Novak
  • John H Morris
  • Courtney A Harper
  • Doug Stryke
  • Scott C H Pegg
  • Sunil Ojha
  • Shoshana Brown
  • Shoshana D Brown
  • Michiko Kawamoto
  • Ranyee A Chiang
  • Ling Song
  • Alexander A Fedorov
  • Steven C Almo
  • Alex S Nord
  • Patricia J Chang
  • Julie Akana
  • Benjamin J Polacco
  • Susan J Johns
  • Stephen G Young
  • William C Skarnes
  • Shelley D Copley
  • Chakrapani Kalyanaraman
  • Heidi J Imker
  • Elena V Fedorov
  • Jennifer L Seffernick
  • Songyan Liu
  • Geoffrey G Hicks
  • Bruce R Conklin
  • Janet Rossant
  • Ken Ichi Yamamura
  • William L Stanford
  • Philippe Soriano
  • Wolfgang Wurst
  • Jennifer Seffernick
  • Ayano Sakai
  • Harald von Melchner
  • Elena Fedorov
  • Antony V Cox
  • Patricia Ruiz
  • Nima Fayazmanesh
  • George L Kenyon
  • Pan Fen Wang
  • Michael J McLeish
  • Leslie A King
  • Pao Tien Chuang
  • Alice Yee
  • Larry L'Italien
  • Roy E Lee

Detail Information

Publications20

  1. pmc A gold standard set of mechanistically diverse enzyme superfamilies
    Shoshana 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...
  2. pmc Comparison of methods for genomic localization of gene trap sequences
    Courtney 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...
  3. ncbi request reprint Definitions of enzyme function for the structural genomics era
    Patricia 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...
  4. doi request reprint Using the Structure-function Linkage Database to characterize functional domains in enzymes
    Shoshana 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...
  5. ncbi request reprint Intersect: identification and visualization of overlaps in database search results
    Scott 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..
  6. ncbi request reprint structureViz: linking Cytoscape and UCSF Chimera
    John 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...
  7. ncbi request reprint Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily
    Margaret 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...
  8. ncbi request reprint Evolution of enzyme superfamilies
    Margaret 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...
  9. ncbi request reprint Prediction and assignment of function for a divergent N-succinyl amino acid racemase
    Ling 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...
  10. pmc Evolution of function in the "two dinucleotide binding domains" flavoproteins
    Sunil 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...
  11. ncbi request reprint Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
    Scott 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...
  12. ncbi request reprint D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily
    Julie 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...
  13. ncbi request reprint Automated discovery of 3D motifs for protein function annotation
    Benjamin J Polacco
    Department of Biopharmaceutical Sciences, University of California, San Francisco, 94143 2250, USA
    Bioinformatics 22:723-30. 2006
    ..This approach allows us to test the assumption that residues that provide function are the most informative for predicting function...
  14. pmc The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse
    Alex S Nord
    University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 34:D642-8. 2006
    ....
  15. ncbi request reprint Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity
    John 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...
  16. ncbi request reprint Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor
    Shelley D Copley
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
    Biochemistry 43:13981-95. 2004
    ....
  17. ncbi request reprint Isoleucine 69 and valine 325 form a specificity pocket in human muscle creatine kinase
    Walter 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...
  18. ncbi request reprint Superfamily active site templates
    Elaine 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
    ....
  19. pmc The Structure Superposition Database
    Ranyee 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...
  20. pmc BayGenomics: a resource of insertional mutations in mouse embryonic stem cells
    Doug 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 Grants11

  1. BMI Bioinformatics Training Grant
    Patricia Babbitt; Fiscal Year: 2007
    ..abstract_text> ..
  2. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2004
    ..abstract_text> ..
  3. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2009
    ..These studies will focus first on superfamilies that use FAD cofactors. ..