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RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction
Guillaume Brysbaert1, Kevin Lorgouilloux1, Wim F Vranken2,3,4
1University of Lille, CNRS UMR8576 UGSF, F-59000 Lille, France.
Bioinformatics (Oxford, England)
|October 14, 2017
Summary
This study introduces RINspector, a Cytoscape app that combines protein residue centrality analysis with flexibility predictions. RINspector aids in identifying key protein residues and predicting mutation effects on flexibility for experimental design.
Area of Science:
- Computational biology
- Structural bioinformatics
- Protein analysis
Background:
- Protein function is dictated by amino acid composition and dynamics.
- Residue interaction networks and centrality analyses identify key residues for protein fold and function.
- These key residues are prime targets for mutagenesis, requiring flexibility data.
Purpose of the Study:
- To develop a tool integrating centrality analysis with residue flexibility predictions.
- To visualize key residues within the context of protein flexibility.
- To predict the impact of mutations on local protein flexibility.
Main Methods:
- Integration of centrality analyses with DynaMine flexibility predictions.
- Development of a Cytoscape application named RINspector.
- Visualization of centrality results on a graph of predicted residue flexibility.
Main Results:
- RINspector successfully combines centrality and flexibility data.
- The app visualizes key residues and their flexibility profiles.
- RINspector enables calculation of mutation effects on local flexibility.
Conclusions:
- RINspector provides a valuable tool for identifying and analyzing key protein residues.
- The app facilitates the design of targeted mutagenesis experiments by predicting flexibility changes.
- RINspector enhances the understanding of protein structure-function relationships.