ProDy: Protein Dynamics Inferred from Theory and Experiments

被引：845

作者：

Bakan, Ahmet ^{[1
]}

Meireles, Lidio M.

Bahar, Ivet

机构：

[1] Univ Pittsburgh, Dept Computat & Syst Biol, Sch Med, Pittsburgh, PA 15213 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 11期

基金：

美国国家卫生研究院;

关键词：

PRINCIPAL COMPONENT ANALYSIS; INTRINSIC DYNAMICS; MOLECULAR-DYNAMICS; DEFORMATION; SUPERFAMILY; FLEXIBILITY; ENZYMES; MOTIONS; MODES;

D O I：

10.1093/bioinformatics/btr168

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods.

引用

页码：1575 / 1577

页数：3

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