Barry J Grant

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi The 2006 automated function prediction meeting
    Ana P C Rodrigues
    Burnham Institute for Medical Research, 10901 N, Torrey Pines Rd, La Jolla, CA 92037 USA
    BMC Bioinformatics 8:S1-4. 2007
  2. ncbi Bio3d: an R package for the comparative analysis of protein structures
    Barry J Grant
    Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
    Bioinformatics 22:2695-6. 2006
  3. ncbi Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain
    Barry J Grant
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
    J Mol Biol 368:1231-48. 2007
  4. ncbi Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
    Barry J Grant
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000325. 2009
  5. ncbi Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
    Denis Bucher
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093, United States
    Biochemistry 50:10530-9. 2011
  6. ncbi Large conformational changes in proteins: signaling and other functions
    Barry J Grant
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA, USA
    Curr Opin Struct Biol 20:142-7. 2010
  7. ncbi Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins
    Alemayehu A Gorfe
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA 92093 0365, USA
    Structure 16:885-96. 2008
  8. ncbi Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics
    Denis Bucher
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California, USA
    PLoS Comput Biol 7:e1002034. 2011
  9. ncbi Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation
    Cesar Augusto F de Oliveira
    Departments of Chemistry and Biochemistry, Howard Hughes Medical Institute, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 7:e1002178. 2011
  10. ncbi Conformational selection in g-proteins: lessons from ras and rho
    Barry J Grant
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California
    Biophys J 99:L87-9. 2010

Collaborators

Detail Information

Publications12

  1. ncbi The 2006 automated function prediction meeting
    Ana P C Rodrigues
    Burnham Institute for Medical Research, 10901 N, Torrey Pines Rd, La Jolla, CA 92037 USA
    BMC Bioinformatics 8:S1-4. 2007
  2. ncbi Bio3d: an R package for the comparative analysis of protein structures
    Barry J Grant
    Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
    Bioinformatics 22:2695-6. 2006
    ..AVAILABILITY: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/..
  3. ncbi Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain
    Barry J Grant
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
    J Mol Biol 368:1231-48. 2007
    ..Our data provide a statistically supported framework for further examination of this and other structure-function relationships in the kinesin family...
  4. ncbi Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
    Barry J Grant
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000325. 2009
    ....
  5. ncbi Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
    Denis Bucher
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093, United States
    Biochemistry 50:10530-9. 2011
    ..As such, they are superior to conventional MD and flexible docking alone and hold great promise for future development and applications to drug discovery...
  6. ncbi Large conformational changes in proteins: signaling and other functions
    Barry J Grant
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA, USA
    Curr Opin Struct Biol 20:142-7. 2010
    ..In particular, a 'conformational selection' picture is emerging, where alterations in the relative populations of pre-existing conformations can best describe the conformational switching activity of these important proteins...
  7. ncbi Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins
    Alemayehu A Gorfe
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA 92093 0365, USA
    Structure 16:885-96. 2008
    ..We identified a number of isoform-specific, long-range side chain interactions that define unique pathways of communication between the nucleotide binding site and the C terminus...
  8. ncbi Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics
    Denis Bucher
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California, USA
    PLoS Comput Biol 7:e1002034. 2011
    ..The study provides a detailed description of the conformational space available to ligand-free MBP, and has implications for understanding ligand recognition and allostery in related proteins...
  9. ncbi Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation
    Cesar Augusto F de Oliveira
    Departments of Chemistry and Biochemistry, Howard Hughes Medical Institute, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 7:e1002178. 2011
    ....
  10. ncbi Conformational selection in g-proteins: lessons from ras and rho
    Barry J Grant
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California
    Biophys J 99:L87-9. 2010
    ..Furthermore, the pattern of correlated motions revealed by these simulations predicts a preserved allosteric coupling of the nucleotide-binding site with the membrane interacting C-terminus in both Rho and Ras...
  11. ncbi Electrostatically biased binding of kinesin to microtubules
    Barry J Grant
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
    PLoS Biol 9:e1001207. 2011
    ..We conclude that electrostatic interactions play an important role in the kinesin stepping mechanism, by biasing the diffusional association of kinesin with microtubules...
  12. ncbi sgTarget: a target selection resource for structural genomics
    Ana P C Rodrigues
    Structural Biology Laboratory, University of York York, YO10 5YW, UK
    Nucleic Acids Res 34:W225-30. 2006
    ....