Elaine C Meng

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Tools for integrated sequence-structure analysis with UCSF Chimera
    Elaine C Meng
    Computer Graphics Laboratory, University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2440, USA
    BMC Bioinformatics 7:339. 2006
  2. 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
  3. 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
  4. pmc UCSF Chimera, MODELLER, and IMP: an integrated modeling system
    Zheng Yang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
    J Struct Biol 179:269-78. 2012
  5. ncbi request reprint UCSF Chimera--a visualization system for exploratory research and analysis
    Eric F Pettersen
    Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143 2240, USA
    J Comput Chem 25:1605-12. 2004
  6. pmc Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies
    Elaine C Meng
    Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94158 2517, USA
    Curr Opin Struct Biol 21:391-7. 2011
  7. pmc Computational tools for the interactive exploration of proteomic and structural data
    John H Morris
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
    Mol Cell Proteomics 9:1703-15. 2010
  8. 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
  9. 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
  10. ncbi request reprint Enhancing UCSF Chimera through web services
    Conrad C Huang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA
    Nucleic Acids Res 42:W478-84. 2014

Collaborators

Detail Information

Publications17

  1. pmc Tools for integrated sequence-structure analysis with UCSF Chimera
    Elaine C Meng
    Computer Graphics Laboratory, University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2440, USA
    BMC Bioinformatics 7:339. 2006
    ..and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals...
  2. 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
    ....
  3. 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...
  4. pmc UCSF Chimera, MODELLER, and IMP: an integrated modeling system
    Zheng Yang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
    J Struct Biol 179:269-78. 2012
    ....
  5. ncbi request reprint UCSF Chimera--a visualization system for exploratory research and analysis
    Eric F Pettersen
    Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143 2240, USA
    J Comput Chem 25:1605-12. 2004
    ..Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/...
  6. pmc Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies
    Elaine C Meng
    Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, CA 94158 2517, USA
    Curr Opin Struct Biol 21:391-7. 2011
    ....
  7. pmc Computational tools for the interactive exploration of proteomic and structural data
    John H Morris
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
    Mol Cell Proteomics 9:1703-15. 2010
    ..We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated exploration of proteomics and structural data...
  8. 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...
  9. 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. ..
  10. ncbi request reprint Enhancing UCSF Chimera through web services
    Conrad C Huang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA
    Nucleic Acids Res 42:W478-84. 2014
    ..Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. ..
  11. 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...
  12. pmc DOCK 6: combining techniques to model RNA-small molecule complexes
    P Therese Lang
    Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94143, USA
    RNA 15:1219-30. 2009
    ..In addition, in the course of the study, we explore a variety of newly added DOCK functions, demonstrating the ease with which new functions can be added to address new scientific questions...
  13. ncbi request reprint Constitutive activation and endocytosis of the complement factor 5a receptor: evidence for multiple activated conformations of a G protein-coupled receptor
    Jennifer L Whistler
    Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California, USA
    Traffic 3:866-77. 2002
    ..Dissociation of two responses normally dependent on agonist binding indicates that the corresponding functions of an activated GPCR reflect different sets of changes in the receptor's conformation...
  14. 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
    ....
  15. 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...
  16. pmc Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target
    Shiming Ye
    Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA
    Proc Natl Acad Sci U S A 102:18700-5. 2005
    ..These findings provide insights into why apoE4 is associated with increased risk for Alzheimer's disease and may represent a potential target for drug development...
  17. ncbi request reprint Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions
    Srinivasan Madabushi
    Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 279:8126-32. 2004
    ..These results define in GPCRs a canonical signal transduction mechanism where ligand binding induces conformational changes propagated through adjacent trigger, linking core, and coupling regions...