ProteinShop: A tool for interactive protein manipulation and steering

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Description

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 ... continued below

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Crivelli, Silvia; Kreylos, Oliver; Max, Nelson; Hamann, Bernd & Bethel, Wes May 25, 2004.

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Description

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.

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Notes

OSTI as DE00836965

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  • Journal Name: Journal of Computer-Aided Molecular Design; Journal Volume: 18; Journal Issue: 4; Other Information: Submitted to Journal of Computer-Aided Molecular Design: Volume 18, No.4; Journal Publication Date: 04/2004

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  • Report No.: LBNL--53731
  • Grant Number: AC03-76SF00098
  • Office of Scientific & Technical Information Report Number: 836965
  • Archival Resource Key: ark:/67531/metadc782994

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  • May 25, 2004

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  • Dec. 3, 2015, 9:30 a.m.

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  • June 22, 2016, 6:34 p.m.

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Crivelli, Silvia; Kreylos, Oliver; Max, Nelson; Hamann, Bernd & Bethel, Wes. ProteinShop: A tool for interactive protein manipulation and steering, article, May 25, 2004; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc782994/: accessed September 21, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.