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. 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. A list of all main features of RINalyzer as well as an overview screenshot can be found here.
RINalyzer is complemented by the RINerator module, which generates user-defined RINs from a 3D protein structure. 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.
A detailed documentation describing RINalyzer and RINerator, as well as storage and format specifications can be found here.
Further useful Cytoscape plugins in addition to RINalyzer:
Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. (2011)
Analyzing and visualizing residue networks of protein structures.
Trends in Biochemical Sciences, 36(4):179-182, doi:10.1016/j.tibs.2011.01.002.
Doncheva, N.T., Assenov, Y., Domingues, F.S., Albrecht, M. (2012)
Topological analysis and interactive visualization of biological networks and protein structures.
Nature Protocols, 7:670-685, doi:10.1038/nprot.2012.004.
Release 1.3 (November 2011) is verified to work with Cytoscape 2.8.x and UCSF Chimera 1.5.x.
Release 1.2 (January 2011) is verified to work with Cytoscape 2.8.0 and the newest version of UCSF Chimera 1.5.
Release 1.1 (September 2010) is verified to work with Cytoscape 2.7.0 and UCSF Chimera 1.2, 1.3, 1.4.
Release 1.0 (September 2010) is verified to work with Cytoscape 2.6.x and UCSF Chimera 1.2, 1.3, 1.4.
For the straightforward download of precomputed RINs for most protein structures deposited in the Protein Data Bank (except for those containing MODELS), we provide a simple web interface here.
All RINs have been generated using the RINerator module, which implements the method described here. The RINerator module can be downloaded here.
Alternatively, the RING web server can be used to easily generate different types of RINs.
Nadezhda T. Doncheva1, Karsten Klein2, Francisco S. Domingues1,3, and Mario Albrecht1
1Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany
2TU Dortmund University, Otto-Hahn-Str. 14, 44227 Dortmund, Germany
3Institute of Genetic Medicine, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
If you have any questions, comments, suggestions or criticism, feel free to contact us at: rinalyzer [at] mpi-inf [dot] mpg [dot] de.