Dina Schneidman-Duhovny

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Accurate SAXS profile computation and its assessment by contrast variation experiments
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
    Biophys J 105:962-74. 2013
  2. pmc A method for integrative structure determination of protein-protein complexes
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:3282-9. 2012
  3. pmc Integrative structural modeling with small angle X-ray scattering profiles
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, USA
    BMC Struct Biol 12:17. 2012
  4. pmc Macromolecular docking restrained by a small angle X-ray scattering profile
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences QB3, University of California at San Francisco, CA 94158, USA
    J Struct Biol 173:461-71. 2011
  5. 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
  6. doi request reprint Modeling of proteins and their assemblies with the integrative modeling platform
    Benjamin Webb
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
    Methods Mol Biol 781:377-97. 2011
  7. pmc Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies
    Daniel Russel
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences QB3, University of California, San Francisco, San Francisco, California, United States of America
    PLoS Biol 10:e1001244. 2012
  8. pmc Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images
    Javier Velázquez-Muriel
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 2552, USA
    Proc Natl Acad Sci U S A 109:18821-6. 2012
  9. doi request reprint ModBase, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Universite Paris Diderot Paris 7, école doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Stanford
    Nucleic Acids Res 42:D336-46. 2014
  10. doi request reprint Modeling of proteins and their assemblies with the Integrative Modeling Platform
    Benjamin Webb
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quanstitative Biosciences QB3, University of California San Francisco, San Francisco, CA, USA
    Methods Mol Biol 1091:277-95. 2014

Collaborators

Detail Information

Publications16

  1. pmc Accurate SAXS profile computation and its assessment by contrast variation experiments
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
    Biophys J 105:962-74. 2013
    ....
  2. pmc A method for integrative structure determination of protein-protein complexes
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
    Bioinformatics 28:3282-9. 2012
    ..On the other hand, computational methods for modeling assembly structures from individual components frequently suffer from high false-positive rate, rarely resulting in a unique solution...
  3. pmc Integrative structural modeling with small angle X-ray scattering profiles
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, USA
    BMC Struct Biol 12:17. 2012
    ..Third, we discuss the use of SAXS profiles in integrative structure modeling approaches that depend simultaneously on several data types...
  4. pmc Macromolecular docking restrained by a small angle X-ray scattering profile
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences QB3, University of California at San Francisco, CA 94158, USA
    J Struct Biol 173:461-71. 2011
    ..Thus, the integrative approach significantly improves on molecular docking alone. The improvement arises from an increased resolution of rigid docking sampling and more accurate scoring...
  5. 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
    ....
  6. doi request reprint Modeling of proteins and their assemblies with the integrative modeling platform
    Benjamin Webb
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
    Methods Mol Biol 781:377-97. 2011
    ..We also demonstrate the Integrative Modeling Platform (IMP) software, which provides the necessary computational framework to implement this protocol, and several applications for specific-use cases...
  7. pmc Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies
    Daniel Russel
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences QB3, University of California, San Francisco, San Francisco, California, United States of America
    PLoS Biol 10:e1001244. 2012
    ....
  8. pmc Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images
    Javier Velázquez-Muriel
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 2552, USA
    Proc Natl Acad Sci U S A 109:18821-6. 2012
    ..Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined...
  9. doi request reprint ModBase, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Universite Paris Diderot Paris 7, école doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Stanford
    Nucleic Acids Res 42:D336-46. 2014
    ....
  10. doi request reprint Modeling of proteins and their assemblies with the Integrative Modeling Platform
    Benjamin Webb
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quanstitative Biosciences QB3, University of California San Francisco, San Francisco, CA, USA
    Methods Mol Biol 1091:277-95. 2014
    ..We also demonstrate the Integrative Modeling Platform (IMP) software, which provides the necessary computational framework to implement this protocol, and several applications for specific use cases. ..
  11. pmc Integrative structure modeling of macromolecular assemblies from proteomics data
    Keren Lasker
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
    Mol Cell Proteomics 9:1689-702. 2010
    ..Correspondingly, integrative computational methods are being developed to provide descriptions of protein complexes at varying levels of accuracy and resolution, ranging from complex compositions to detailed atomic structures...
  12. pmc Statistical potential for modeling and ranking of protein-ligand interactions
    Hao Fan
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
    J Chem Inf Model 51:3078-92. 2011
    ..The statistical potentials are available through the Integrative Modeling Platform (IMP) software package (http://salilab.org/imp) and the LigScore Web server (http://salilab.org/ligscore/)...
  13. pmc Optimized atomic statistical potentials: assessment of protein interfaces and loops
    Guang Qiang Dong
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences QB3, University of California, San Francisco, CA 94158, USA
    Bioinformatics 29:3158-66. 2013
    ..Here, we formulate the statistical potentials entirely within a statistical framework, avoiding questionable statistical mechanical assumptions and approximations, including a definition of the reference state...
  14. pmc FoXS: a web server for rapid computation and fitting of SAXS profiles
    Dina Schneidman-Duhovny
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 38:W540-4. 2010
    ..Here, we describe the interface and capabilities of the FoXS web server (http://salilab.org/foxs)...
  15. pmc ModBase, a database of annotated comparative protein structure models, and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158, USA
    Nucleic Acids Res 39:D465-74. 2011
    ..org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs)...
  16. pmc The structural dynamics of macromolecular processes
    Daniel Russel
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158 2330, USA
    Curr Opin Cell Biol 21:97-108. 2009
    ..We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes...