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Bioinformatics Advance Access originally published online on July 10, 2007
Bioinformatics 2007 23(17):2345-2347; doi:10.1093/bioinformatics/btm329
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

structureViz: linking Cytoscape and UCSF Chimera

John H. Morris 1,*, Conrad C. Huang 1, Patricia C. Babbitt 2,1 and Thomas E. Ferrin 1,2

1Department of Pharmaceutical Chemistry and 2Department of Biopharmaceutical Sciences, University of California, San Francisco, USA

*To whom correspondence should be addressed.


  Abstract

Summary: structureViz is a Cytoscape plug-in that links the visualization of biological networks provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera. When combined with Cytoscape and Chimera, structureViz provides the first tool that links these two critical aspects of computational analysis in a straightforward manner. structureViz includes commands to open structures in Chimera and align them using Chimera's sequence-structure analysis tools. When a structure is opened, structureViz provides an alternative interface to Chimera: the Cytoscape Molecular Structure Navigator. This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains and residues, mostly through the use of context menus.

Contact: scooter{at}cgl.ucsf.edu

Associate Editor: Thomas Lengauer

Received on February 28, 2007; revised on May 29, 2007; accepted on June 16, 2007

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