Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces

被引：218

作者：

Seeber, Michele ^{[1
,2
]}

Felline, Angelo ^{[1
]}

Raimondi, Francesco ^{[1
,2
]}

Muff, Stefanie ^{[3
]}

Friedman, Ran ^{[3
]}

Rao, Francesco ^{[4
]}

Caflisch, Amedeo ^{[3
]}

Fanelli, Francesca ^{[1
,2
]}

机构：

[1] Univ Modena & Reggio Emilia, Dipartimento Chim, I-41125 Modena, Italy

[2] Univ Modena & Reggio Emilia, DTI, I-41125 Modena, Italy

[3] Univ Zurich, Dept Biochem, CH-8057 Zurich, Switzerland

[4] Univ Freiburg, FRIAS, D-79104 Freiburg, Germany

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2011年 / 32卷 / 06期

基金：

瑞士国家科学基金会;

关键词：

structural/dynamics analysis program; free energy landscape; elastic network model; protein structure network; communication paths; NORMAL-MODE ANALYSIS; BETA-SHEET MINIPROTEIN; PROTEIN STRUCTURES; DYNAMICS SIMULATIONS; NETWORK ANALYSIS; SECONDARY STRUCTURE; SINGLE-PARAMETER; RESIDUES; PACKAGE; IDENTIFICATION;

D O I：

10.1002/jcc.21688

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 1183-1194, 2011

引用

页码：1183 / 1194

页数：12

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