The Cytoscape 3.1 version of RINalyzer has been greatly extended with new functionality and is now using the [http://apps.cytoscape.org/apps/structureViz2 structureViz2 app] commands to interact with UCSF Chimera. Among others, the new features include automatic import, generation and annotation of RINs as well as new and user-friendly means to explore and compare RINs.
For a brief introduction of the new features click [http://rinalyzer.de/docu/app_features.php here].
RINalyzer provides a number of important methods for analyzing and visualizing residue interaction networks (RINs). A RIN is constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. Network nodes and edges represent amino acid residues and their molecular interactions, respectively. The network topology of RINs is normally characterized by undirected and weighted interaction edges between residue nodes. RINalyzer is a Java plugin for Cytoscape, a free software platform for the analysis and visualization of molecular interaction networks.
RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in Cytoscape, together with the corresponding molecular 3D structure visualized in UCSF Chimera. Furthermore, RINalyzer offers the computation and illustration of a comprehensive set of weighted centrality measures for relating spatially distant residue nodes and discovering critical residues and their long-range interaction paths in protein structures. In addition, RINalyzer allows handling node sets, i.e., sets of selected nodes, for analyzing structural and functional connections between different nodes (replaced and extended in Cytoscape 3 by the [http://apps.cytoscape.org/apps/setsapp setsApp]). Another feature is the network comparison of aligned protein structures by constructing a combined RIN, which enables the detailed comparative analysis of residue interactions in different proteins.