Evol and ProDy for bridging protein sequence evolution and structural dynamics

Ahmet Bakan; Anindita Dutta; Wenzhi Mao; Ying Liu; Chakra Chennubhotla; Timothy R. Lezon; Ivet Bahar

doi:10.1093/bioinformatics/btu336

Evol and ProDy for bridging protein sequence evolution and structural dynamics

Ahmet Bakan
, Anindita Dutta
, Wenzhi Mao
, Ying Liu
, Chakra Chennubhotla
, Timothy R. Lezon
, Ivet Bahar

Laufer Center for Physical and Quantitative Biology

University of Pittsburgh

Research output: Contribution to journal › Article › peer-review

192 Scopus citations

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/.

Original language	English
Pages (from-to)	2681-2683
Number of pages	3
Journal	Bioinformatics
Volume	30
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/btu336
State	Published - Sep 15 2014

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title = "Evol and ProDy for bridging protein sequence evolution and structural dynamics",

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/.",

author = "Ahmet Bakan and Anindita Dutta and Wenzhi Mao and Ying Liu and Chakra Chennubhotla and Lezon, \{Timothy R.\} and Ivet Bahar",

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year = "2014",

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doi = "10.1093/bioinformatics/btu336",

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T1 - Evol and ProDy for bridging protein sequence evolution and structural dynamics

AU - Bakan, Ahmet

AU - Dutta, Anindita

AU - Mao, Wenzhi

AU - Liu, Ying

AU - Chennubhotla, Chakra

AU - Lezon, Timothy R.

AU - Bahar, Ivet

PY - 2014/9/15

Y1 - 2014/9/15

N2 - 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/.

AB - 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/.

UR - https://www.scopus.com/pages/publications/84907486031

U2 - 10.1093/bioinformatics/btu336

DO - 10.1093/bioinformatics/btu336

M3 - Article

C2 - 24849577

AN - SCOPUS:84907486031

SN - 1367-4803

VL - 30

SP - 2681

EP - 2683

JO - Bioinformatics

JF - Bioinformatics

IS - 18

ER -

Evol and ProDy for bridging protein sequence evolution and structural dynamics

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