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RINalyzer

Description

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.

A tutorial for the first steps of using RINalyzer is available here. Further information and tutorials on using Cytoscape are available here.

Further useful Cytoscape plugins in addition to RINalyzer:

  • NetworkAnalyzer performs analysis of biological networks and calculates network topology parameters.
  • NeighborHighlight highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
  • ShortestPath shows the shortest path between two selected nodes in the current network.
  • HiderSlider allows a user to interactively explore a network by hiding/showing nodes or edges with attribute values above an adjustable threshold using a slider bar.
  • EdgeLister provides a means of tracking edge selection.
  • RandomNetworks can be used to generate random networks, randomize existing networks and compare existing networks to random models.
  • Clustering:
    • clusterViz is a plugin for clustering biological networks using the FAG-EC, EAGLE or MCODE algorithms.
    • MCODE finds clusters (highly interconnected regions) in a network.
    • clusterMaker unifies different clustering techniques (MCL and FORCE) and displays them in a single interface and clusterExplorer may be used to explore the cluster statistics and relationships.
    • CytoMCL clusters networks using the MCL clustering algorithm.


Reference

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.


Tutorial

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.


Releases

You can download the latest release of RINalyzer here. If you have trouble installing RINalyzer, you can read further instructions here.

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.


RIN Data

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.


Contributors

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


Contact

If you have any questions, comments, suggestions or criticism, feel free to contact us at: rinalyzer [at] mpi-inf [dot] mpg [dot] de.