Patricia Babbitt

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The Structure-Function Linkage Database
    Eyal Akiva
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Santiago 8370146, Chile, Nodality, Inc, South San Francisco, CA 94080, USA, Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, MA 02215, USA, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA, Center for Bioinformatics ZBH, University of Hamburg, Hamburg 20146, Germany, Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA, UC Berkeley UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158 and Berkeley, CA 94720, USA and California Institute for Quantitative Biosciences, University of California, San Francisco, Canada
    Nucleic Acids Res 42:D521-30. 2014
  2. pmc Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies
    Ranyee A Chiang
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 4:e1000142. 2008
  3. pmc Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
    Holly J Atkinson
    Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e4345. 2009
  4. pmc A mapping of drug space from the viewpoint of small molecule metabolism
    James Corey Adams
    Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, California, USA
    PLoS Comput Biol 5:e1000474. 2009
  5. pmc Glutathione transferases are structural and functional outliers in the thioredoxin fold
    Holly J Atkinson
    Program in Biological and Medical Informatics, University of California, San Francisco, California 94158 2330, USA
    Biochemistry 48:11108-16. 2009
  6. pmc An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations
    Holly J Atkinson
    Graduate Program in Biological and Medical Informatics, University of California, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000541. 2009
  7. pmc Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    Alexandra M Schnoes
    Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000605. 2009
  8. pmc Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function
    Daniel E Almonacid
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 6:e1000700. 2010
  9. pmc Pythoscape: a framework for generation of large protein similarity networks
    Alan E Barber
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:2845-6. 2012
  10. 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

Research Grants

  1. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2001
  2. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2008
  3. BMI Bioinformatics Training Grants
    Patricia Babbitt; Fiscal Year: 2008
  4. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2007
  5. BMI Bioinformatics Training Grant
    Patricia Babbitt; Fiscal Year: 2007
  6. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2006
  7. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2005
  8. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2004
  9. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2003
  10. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2002

Collaborators

  • John H Morris
  • Thomas E Ferrin
  • Andrej Sali
  • Elaine C Meng
  • JOHN GERLT
  • Matthew P Jacobson
  • Shoshana D Brown
  • John B O Mitchell
  • Holly J Atkinson
  • Conrad C Huang
  • Doug Stryke
  • Margaret E Glasner
  • Ranyee A Chiang
  • Sunil Ojha
  • Walter R P Novak
  • Alan E Barber
  • Daniel E Almonacid
  • Alexandra M Schnoes
  • Courtney A Harper
  • Scott C H Pegg
  • Eyal Akiva
  • Michiko Kawamoto
  • James Corey Adams
  • Ling Song
  • Steven C Almo
  • Alexander A Fedorov
  • Alex S Nord
  • Patricia J Chang
  • Julie Akana
  • Benjamin J Polacco
  • William C Skarnes
  • Susan J Johns
  • Stephen G Young
  • Shelley D Copley
  • David Mischel
  • Michael A Hicks
  • Susan T Mashiyama
  • Ashley F Custer
  • Jeffrey M Yunes
  • Gemma L Holliday
  • Florian Lauck
  • Emmanuel R Yera
  • Deok Sun Lee
  • Henry F Chambers
  • Michael J Keiser
  • Igor Dodevski
  • Li Basuino
  • OLAF G WIEST
  • Heidi J Imker
  • Chakrapani Kalyanaraman
  • Elena V Fedorov
  • Geoffrey G Hicks
  • Elena Fedorov
  • Janet Rossant
  • Jennifer Seffernick
  • Antony V Cox
  • Bruce R Conklin
  • William L Stanford
  • Philippe Soriano
  • Harald von Melchner
  • Patricia Ruiz
  • Wolfgang Wurst
  • Nima Fayazmanesh
  • Songyan Liu
  • Ken Ichi Yamamura
  • Ayano Sakai
  • Pan Fen Wang
  • George L Kenyon
  • Michael J McLeish
  • Leslie A King
  • Pao Tien Chuang
  • Larry L'Italien
  • Roy E Lee
  • Alice Yee

Detail Information

Publications29

  1. pmc The Structure-Function Linkage Database
    Eyal Akiva
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Santiago 8370146, Chile, Nodality, Inc, South San Francisco, CA 94080, USA, Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, MA 02215, USA, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA, Center for Bioinformatics ZBH, University of Hamburg, Hamburg 20146, Germany, Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA, UC Berkeley UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158 and Berkeley, CA 94720, USA and California Institute for Quantitative Biosciences, University of California, San Francisco, Canada
    Nucleic Acids Res 42:D521-30. 2014
    ..The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. ..
  2. pmc Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies
    Ranyee A Chiang
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 4:e1000142. 2008
    ..Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies...
  3. pmc Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
    Holly J Atkinson
    Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e4345. 2009
    ..As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships...
  4. pmc A mapping of drug space from the viewpoint of small molecule metabolism
    James Corey Adams
    Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, California, USA
    PLoS Comput Biol 5:e1000474. 2009
    ..Thus, this work provides a large-scale approach to ligand-based prediction of drug action in small molecule metabolism...
  5. pmc Glutathione transferases are structural and functional outliers in the thioredoxin fold
    Holly J Atkinson
    Program in Biological and Medical Informatics, University of California, San Francisco, California 94158 2330, USA
    Biochemistry 48:11108-16. 2009
    ....
  6. pmc An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations
    Holly J Atkinson
    Graduate Program in Biological and Medical Informatics, University of California, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000541. 2009
    ..The unifying context provided by this work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relationships, illustrated here with the thioredoxins and peroxiredoxins...
  7. pmc Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    Alexandra M Schnoes
    Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 5:e1000605. 2009
    ..Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation...
  8. pmc Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function
    Daniel E Almonacid
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 6:e1000700. 2010
    ..The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation...
  9. pmc Pythoscape: a framework for generation of large protein similarity networks
    Alan E Barber
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:2845-6. 2012
    ....
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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..
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  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. 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
    ....
  21. 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...
  22. 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
    ....
  23. 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...
  24. 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
    ....
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2001
    ..abstract_text> ..
  2. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2008
    ..These studies will focus first on superfamilies that use FAD cofactors. ..
  3. BMI Bioinformatics Training Grants
    Patricia Babbitt; Fiscal Year: 2008
    ..a computational perspective to pharmacogenomics studies aimed at understanding differences in human response to drug therapy or by analyzing whole genome expression patterns to identify new drug targets for diseases such as malaria ..
  4. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2007
    ..These studies will focus first on superfamilies that use FAD cofactors. ..
  5. BMI Bioinformatics Training Grant
    Patricia Babbitt; Fiscal Year: 2007
    ..abstract_text> ..
  6. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2006
    ..These studies will focus first on superfamilies that use FAD cofactors. ..
  7. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2005
    ..These studies will focus first on superfamilies that use FAD cofactors. ..
  8. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2004
    ..abstract_text> ..
  9. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2003
    ..abstract_text> ..
  10. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2002
    ..abstract_text> ..
  11. LAYING THE FOUNDATION FOR GENOMIC ENZYMOLOGY
    Patricia Babbitt; Fiscal Year: 2009
    ..These studies will focus first on superfamilies that use FAD cofactors. ..