RINspector is an app that performs centrality analyses on residue interaction networks (RIN) and retrieves DynaMine flexibility predictions of protein chains.
A residue interaction network can be created from a 3D structure with Chimera through the structureViz app (the additional RINalyzer app permits to layout the network in function of the 3D coordinates of the residues) or directly imported. It is a network in which nodes are residues and edges interactions between residues, detected in the structure.
The centrality analyses that can be performed are based on shortest path lengths, the network is considered unweighted and undirected. They are of 3 types : (i) residue centrality analyses that rely on the change in average shortest path length under removal of individual nodes (cf del Sol et al. Mol Syst Biol 2006), (ii) betweenness centrality analyses and (iii) closeness centrality analyses. A Z-score is calculated for each centrality analysis.
This app enhances centrality analyses with DynaMine flexibility predictions. It connects to the DynaMine server to retrieve the backbone dynamics of a selected protein chain and the flexibility graph is displayed in the result panel. Residues can be selected in this graph, the network, and in the structure with Chimera/structureViz. They can then be mutated to predict dynamics of mutated sequences. The selection of residues in one of the 3 views (network, flexibility graph, structure) automatically highlights them in the other two, which permits a direct visualization of their context.
Centrality analyses and DynaMine predictions can be performed through the app menu, through the command dialog or through the automation facilities provided by Cytoscape 3.6 via the Help/Automation/CyREST Command API menu.
The combination of centrality analysis, flexibility predictions of wild and mutated sequences and potentially other analyses from other apps like RINalyzer permits to get a fast glance at residues that are essential for the function of proteins.
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**Citations**
Guillaume Brysbaert, Kevin Lorgouilloux, Wim F Vranken, Marc F Lensink<br />
***RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction***<br />
Bioinformatics, 2017, btx586, https://doi.org/10.1093/bioinformatics/btx586
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For automation:<br /><br />
Guillaume Brysbaert, Théo Mauri, Marc F Lensink<br />
***Comparing protein structures with RINspector automation in Cytoscape***<br />
F1000research, 2018, https://f1000research.com/articles/7-563/
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**Tutorial**
The latest created tutorial is in the article:<br /><br />
Guillaume Brysbaert, Théo Mauri, Jérôme de Ruyck, Marc F Lensink<br />
***Identification of Key Residues in Proteins Through Centrality Analysis and Flexibility Prediction with RINspector***.<br />
Curr Protoc Bioinformatics. 2018 Nov 29:e66. doi: 10.1002/cpbi.66.<br />
https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpbi.66
An example of application was already given in the RINspector article. An example for automation application is given in the RINspector automation article (with scripts).
A last tutorial on another case (with sample file) is given in the step-by-step tutorial accessible here: http://ugsf.univ-lille1.fr/RINspector-443?lang=en
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**Links**
Initial article that contains examples of application of the residue centrality analysis that relies on the change in average shortest path length under removal of individual nodes:
del Sol A, Fujihashi H, Amoros D, Nussinov R.<br />
***Residues crucial for maintaining short paths in network communication mediate signaling in proteins.***<br />
Mol Syst Biol., 2006; http://msb.embopress.org/content/2/1/2006.0019.long
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Article that describes the DynaMine flexibility prediction method:
Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, and Wim Vranken<br />
***From protein sequence to dynamics and disorder with DynaMine***<br />
Nature Communications 2013, https://www.nature.com/articles/ncomms3741
and the one of the webserver ( http://dynamine.ibsquare.be/ ) that can be directly queried with a protein sequence
Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, and Wim Vranken<br />
***The DynaMine webserver: predicting protein dynamics from sequence***<br />
Nucleic Acid Research 2014, https://academic.oup.com/nar/article/42/W1/W264/2435183
