Software tools for analysis and visulaization of protein structure

Summary

Principal Investigator: Ethan Merritt
Abstract: This project encompasses the continued development, evaluation, maintenance, distribution, and support of software tools relating to protein structure. The widely-used structural visualization tools in the RasterSD package will be brought up to date for use on current operating systems, and extended to incorporate new visualization modes made possible by a new generation of analysis tools. Existing web-based services provided by this group to the research community at large (WebTools, Parvati, TLSMD) will be updated and server capacity expanded. A major goal of the project is to further extend and distribute the recently developed TLSMD software package for the inference of protein flexibility and other dynamic properties directly from previously refined single crystal structures. The core software components will be adapted for incorporation into standard protein crystallographic packages so that TLSMD analysis may be installed and used locally crystallographic research groups. The central TLSMD server will be expanded to handle the demands of researchers in other fields, who are not expected to have crystallographic software installed locally. The core TLSMD algorithms will be extended and adapted for use outside the applications in crystallographic refinement for which it was originally developed. In particular, it will be extended to generate models of protein flexibility for use in protein-ligand and protein-protein docking calculations.These analytical techniques will be applied to all structures in the Protein Data Bank in order to build a comprehensive database of implied domain motions, hinge points, and dynamic behavior. The algorithms and computation tools developed as part of this work will be distributed freely, and we will provide web-based state of the art analysis of structures submitted by external researchers.
Funding Period: ----------------2007 - ---------------2011-
more information: NIH RePORT

Top Publications

  1. pmc Atomic resolution studies of carbonic anhydrase II
    Craig A Behnke
    Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195 7430, USA
    Acta Crystallogr D Biol Crystallogr 66:616-27. 2010
  2. pmc Validation of crystallographic models containing TLS or other descriptions of anisotropy
    Frank Zucker
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 66:889-900. 2010
  3. pmc Some B(eq) are more equivalent than others
    Ethan A Merritt
    Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr A 67:512-6. 2011
  4. pmc To B or not to B: a question of resolution?
    Ethan A Merritt
    Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 68:468-77. 2012

Scientific Experts

  • Ethan Merritt
  • Frank Zucker
  • Craig A Behnke
  • David C Teller
  • P Christoph Champ
  • Isolde Le Trong
  • Jurgen Bajorath
  • Jeff W Godden
  • Ronald E Stenkamp

Detail Information

Publications4

  1. pmc Atomic resolution studies of carbonic anhydrase II
    Craig A Behnke
    Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195 7430, USA
    Acta Crystallogr D Biol Crystallogr 66:616-27. 2010
    ..These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available...
  2. pmc Validation of crystallographic models containing TLS or other descriptions of anisotropy
    Frank Zucker
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 66:889-900. 2010
    ..Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface...
  3. pmc Some B(eq) are more equivalent than others
    Ethan A Merritt
    Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr A 67:512-6. 2011
    ..In particular, it may lead to improved selection of multi-group TLS models based on analysis of an initial isotropic refinement...
  4. pmc To B or not to B: a question of resolution?
    Ethan A Merritt
    Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 68:468-77. 2012
    ....