Department of Computer Science & Engineering, Polytechnic Institute of NYU, Brooklyn, NY 11201, USA.
Department of Biochemistry and Molecular Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
Structure. 2015 May 5;23(5):941-948. doi: 10.1016/j.str.2015.02.013. Epub 2015 Apr 9.
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.
以网络表示形式查看生物数据（例如大型复合物内的蛋白质-蛋白质相互作用），并结合单个分子实体的三维结构可视化，这可能会很有帮助。这里介绍的 CyToStruct 在 Cytoscape 网络分析平台和分子查看器（包括 PyMOL、UCSF Chimera、VMD 和 Jmol）之间提供了透明的接口。CyToStruct 从网络的边缘和节点启动并将脚本传递给分子查看器。我们提供了演示，以分析大型蛋白质/RNA/DNA 复合物中亚基之间的相互作用，以及蛋白质之间的相似性。CyToStruct 通过添加结构分析层来丰富 Cytoscape 的网络工具，提供了分子查看器中实现的所有功能。CyToStruct 可在 https://bitbucket.org/sergeyn/cytostruct/wiki/Home 和 Cytoscape App Store 中获得。给定分子复合物的坐标，我们的 Web 服务器（http://trachel-srv.cs.haifa.ac.il/rachel/ppi/）会自动生成所有文件，以将复合物可视化为带有 CyToStruct 桥接到 PyMOL、UCSF Chimera、VMD 和 Jmol 的 Cytoscape 网络。
