ProteinShop: A tool for interactive protein manipulation and steering
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.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE; National Science Foundation Contracts CHE-0205170 and ACI 9624034, National Institute of Health Contract P20 MH60975-06A2. National Institute of Mental Health and National Science Foundation; Large Scientific and Software Data Set Visualization Program Contract ACI 9982251, National Partnership for Advanced Computational Infrastructure, Information Technology Research Grant (US)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 836965
- Report Number(s):
- LBNL-53731; R&D Project: 365963; TRN: US200504%%430
- Journal Information:
- Journal of Computer-Aided Molecular Design, Vol. 18, Issue 4; Other Information: Submitted to Journal of Computer-Aided Molecular Design: Volume 18, No.4; Journal Publication Date: 04/2004; PBD: 25 May 2004
- Country of Publication:
- United States
- Language:
- English
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