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Journal of Computer-Aided Molecular Design

, Volume 18, Issue 4, pp 271–285 | Cite as

ProteinShop: A tool for interactive protein manipulation and steering

  • Silvia Crivelli
  • Oliver Kreylos
  • Bernd Hamann
  • Nelson Max
  • Wes Bethel
Article

Abstract

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.

interactive methods inverse kinematics molecular visualization protein manipulation 

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Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Silvia Crivelli
    • 1
  • Oliver Kreylos
    • 2
  • Bernd Hamann
    • 2
  • Nelson Max
    • 2
  • Wes Bethel
    • 1
  1. 1.Computational Research DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  2. 2.Department of Computer ScienceUniversity of CaliforniaDavisUSA

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