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      CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers.

      1 , 2 , 3

      Structure (London, England : 1993)

      Elsevier BV

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          Abstract

          It can be informative to view biological data, e.g., protein-protein interactions within a large complex, in a network representation coupled with three-dimensional structural visualizations of individual molecular entities. CyToStruct, introduced here, provides a transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. We provide demonstrations to analyze interactions among subunits in large protein/RNA/DNA complexes, and similarities among proteins. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. CyToStruct is available at https://bitbucket.org/sergeyn/cytostruct/wiki/Home and in the Cytoscape App Store. Given the coordinates of a molecular complex, our web server (http://trachel-srv.cs.haifa.ac.il/rachel/ppi/) automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol.

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          Author and article information

          Journal
          Structure
          Structure (London, England : 1993)
          Elsevier BV
          1878-4186
          0969-2126
          May 05 2015
          : 23
          : 5
          Affiliations
          [1 ] Department of Computer Science & Engineering, Polytechnic Institute of NYU, Brooklyn, NY 11201, USA.
          [2 ] Department of Biochemistry and Molecular Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel. Electronic address: bental@tauex.tau.ac.il.
          [3 ] Department of Computer Science, University of Haifa, Mount Carmel 31905, Israel. Electronic address: trachel@cs.haifa.ac.il.
          Article
          S0969-2126(15)00076-3
          10.1016/j.str.2015.02.013
          25865247

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