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

TitleWordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
Publication TypeJournal Article
Year of Publication2011
AuthorsSeeber M., Felline A., Raimondi F., Muff S., Friedman R., Rao F., Caflisch A., Fanelli F.
JournalJournal of Computational Chemistry
Volume32
Issue6
Pagination1183-1194
Date Published2011 Apr 30
Type of ArticleResearch Article
ISSN1096-987X
KeywordsAlgorithms, Animals, Kinetics, Models, Molecular, Molecular Structure, Peptides, Proteins, Software, Surface Properties, Thermodynamics, Vibration
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.

DOI10.1002/jcc.21688
pubindex

0143

Alternate JournalJ. Comput. Chem.
PubMed ID21387345
PubMed Central IDPMC3151548
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