VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability

Bioinformatics
Prakash Chandra RathiHolger Gohlke

Abstract

Constraint network analysis (CNA) is a graph theory-based rigidity analysis approach for linking a biomolecule's structure, flexibility, (thermo)stability and function. Results from CNA are highly information-rich and require intuitive, synchronized and interactive visualization for a comprehensive analysis. We developed VisualCNA, an easy-to-use PyMOL plug-in that allows setup of CNA runs and analysis of CNA results linking plots with molecular graphics representations. From a practical viewpoint, the most striking feature of VisualCNA is that it facilitates interactive protein engineering aimed at improving thermostability. VisualCNA and its dependencies (CNA and FIRST software) are available free of charge under GPL and academic licenses, respectively. VisualCNA and CNA are available at http://cpclab.uni-duesseldorf.de/software; FIRST is available at http://flexweb.asu.edu.

References

Nov 27, 1995·Physical Review Letters·D J Jacobs, M F Thorpe
Jun 8, 2001·Proteins·D J JacobsM F Thorpe
Jan 20, 2011·Proteins·Sebastian Radestock, Holger Gohlke
Feb 14, 2012·Journal of Biotechnology·Prakash C RathiHolger Gohlke
Sep 26, 2012·Journal of Computational Chemistry·Christopher PflegerHolger Gohlke

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Citations

Mar 24, 2016·PLoS Computational Biology·Prakash Chandra RathiHolger Gohlke
Dec 1, 2017·Briefings in Bioinformatics·Aitor Blanco-MíguezAnália Lourenço
Mar 1, 2020·International Journal of Molecular Sciences·Francisca ContrerasMehdi D Davari
Jan 7, 2020·Journal of Chemical Information and Modeling·Christina NutschelHolger Gohlke

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