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. 2014 Sep 15;30(18):2681-3.
doi: 10.1093/bioinformatics/btu336. Epub 2014 May 21.

Evol and ProDy for bridging protein sequence evolution and structural dynamics

Ahmet Bakan  1 , Anindita Dutta  1 , Wenzhi Mao  1 , Ying Liu  1 , Chakra Chennubhotla  1 , Timothy R Lezon  1 , Ivet Bahar  1
Affiliations
Free PMC article

Evol and ProDy for bridging protein sequence evolution and structural dynamics

Ahmet Bakan et al. Bioinformatics. .
Free PMC article

Abstract

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics.

Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/.

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Figures

Fig. 1.
Fig. 1.
NMWiz for comparative analysis of ProDy and Evol output. (A) NMWiz control panel. (B) Protein and normal mode representations, (C) mobility and conservation profiles and (D) cross-correlations in dynamics and coevolution generated via NMWiz
Fig. 2.
Fig. 2.
Comparison of sequence conservation and residue mobility (panels A and B), and sequence-coevolution and spatial location of selected coevolving pairs (panels C and D) for RNase A. See text in Section 2.6 for more details
See this image and copyright information in PMC

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