title: CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers.
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.
authors: Department of Computer Science & Engineering, Polytechnic Institute of NYU, Brooklyn, NY 11201, USA.
authors: Sergey
authors: S
authors: Nepomnyachiy
authors: 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.
authors: Nir
authors: N
authors: Ben-Tal
authors: Department of Computer Science, University of Haifa, Mount Carmel 31905, Israel. Electronic address: trachel@cs.haifa.ac.il.
authors: Rachel
authors: R
authors: Kolodny
mesh_terms: D019295:Computational Biology / Q000379:methods*; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D011506:Proteins