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Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces


Seeber, M; Felline, A; Raimondi, F; Muff, S; Friedman, R; Rao, F; Caflisch, A; Fanelli, F (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry, 32(6):1183-1194.

Abstract

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. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.

Abstract

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. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Date:2011
Deposited On:24 Mar 2011 16:16
Last Modified:07 Dec 2017 08:08
Publisher:Wiley-Blackwell
ISSN:0192-8651
Publisher DOI:https://doi.org/10.1002/jcc.21688
PubMed ID:21117094

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