Evol and ProDy for bridging protein sequence evolution and structural dynamics.
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.


METHODS
ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/.
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Ahmet
A
Bakan
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Anindita
A
Dutta
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Wenzhi
W
Mao
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Ying
Y
Liu
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Chakra
C
Chennubhotla
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Timothy R
TR
Lezon
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Ivet
I
Bahar
D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment; D012984:Software
D011506:Proteins