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

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 acc...

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Bibliographic Details
Published in:Journal of computational chemistry Vol. 32; no. 6; pp. 1183 - 1194
Main Authors: Seeber, Michele, Felline, Angelo, Raimondi, Francesco, Muff, Stefanie, Friedman, Ran, Rao, Francesco, Caflisch, Amedeo, Fanelli, Francesca
Format: Journal Article
Language:English
Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 30.04.2011
Wiley Subscription Services, Inc
Subjects:
Algorithms
Analytical chemistry
Animals
communication paths
elastic network model
free energy landscape
Kinetics
Models, Molecular
Molecular chemistry
Molecular Structure
Molecules
Peptides - chemistry
protein structure network
Proteins
Proteins - chemistry
Software
Software and Updates
structural/dynamics analysis program
Surface Properties
Thermodynamics
Vibration
ISSN:0192-8651, 1096-987X, 1096-987X
Online Access:Get full text
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Summary: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.
Bibliography:http://dx.doi.org/10.1002/jcc.21688
ArticleID:JCC21688
ark:/67375/WNG-Z5XF7M6D-N
Swiss National Science Foundation
Telethon-Italy Grant - No. S00068TELU
istex:03F9E83CED1FEECC1D9A36DE645F163BA48F3451
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Contract/grant sponsor: Telethon-Italy Grant; contract/grant number: S00068TELU
Contract/grant sponsor: Swiss National Science Foundation
School of Natural Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden
ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.21688