Release 1.2 (January 2011) is verified to work with Cytoscape 2.8.0 and the newest version of UCSF Chimera 1.5. Release 1.3 (November 2011) is verified to work with Cytoscape 2.8.x and UCSF Chimera 1.5.x. Release 2.0 (June 2014) is verified to work with Cytoscape 3.1.x and UCSF Chimera 1.8.1 (and above). If you have trouble installing RINalyzer, you can read further instructions here.
#Cytoscape 3 tutorial download#
For Cytoscape 3.x, you also need to download structureViz. You can download the latest release of RINalyzer here.
Integrative visual analysis of protein sequence mutations.īMC Proceedings, 8(Suppl 2):S2, doi:10.1186/1753-6561-8-S2-S2. Topological analysis and interactive visualization of biological networks and protein structures. (2011)Īnalyzing and visualizing residue networks of protein structures. Further information and tutorials on using Cytoscape are available here.ĭoncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. Since version 2.0 RINalyzer is using the structureViz2 app to interact with UCSF Chimera and both apps complement each other.Ī detailed documentation as well as storage and format specifications can be found here.Ī tutorial for the first steps of using RINalyzer is available here.
In contrast to previous simplistic interaction definition approaches based on spatial atomic distance between residues, RINerator enables a more realistic representation by considering different biochemical interaction types and even quantifying the strength of individual interactions. RINalyzer is complemented by the RINerator module, which generates user-defined RINs from a 3D protein structure. A list of all main features of RINalyzer as well as an overview screenshot can be found here. In addition, RINalyzer supports the interactive exploration by providing easy-to-use filters and the generation of subnetworks and aggregated networks. 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. 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. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in Cytoscape, together with the corresponding molecular 3D structure visualized in UCSF Chimera.
#Cytoscape 3 tutorial software#
RINalyzer is a Java plugin for Cytoscape, a free software platform for the analysis and visualization of molecular interaction networks. The network topology of RINs is normally characterized by undirected and weighted interaction edges between residue nodes. Network nodes and edges represent amino acid residues and their molecular interactions, respectively.
A RIN is constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer provides a number of important methods for analyzing and visualizing residue interaction networks (RINs). Our poster at VIZBI 2014 (abstract available here).
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