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Topological Analysis and Interactive Visualization of Biological Networks and Protein Structures

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons44342

Doncheva,  Nadezhda Tsankova
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons44040

Assenov,  Yassen
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons43993

Albrecht,  Mario
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

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Citation

Doncheva, N. T., Assenov, Y., Domingues, F. S., & Albrecht, M. (2012). Topological Analysis and Interactive Visualization of Biological Networks and Protein Structures. Nature Protocols, 7(4), 670-685. doi:10.1038/nprot.2012.004.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-C9C0-B
Abstract
Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in approximately 2 h.