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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Wiley Subscription Services, Inc., A Wiley Company
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151548/ https://www.ncbi.nlm.nih.gov/pubmed/21387345 http://dx.doi.org/10.1002/jcc.21688 |
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author | Seeber, Michele Felline, Angelo Raimondi, Francesco Muff, Stefanie Friedman, Ran Rao, Francesco Caflisch, Amedeo Fanelli, Francesca |
author_facet | Seeber, Michele Felline, Angelo Raimondi, Francesco Muff, Stefanie Friedman, Ran Rao, Francesco Caflisch, Amedeo Fanelli, Francesca |
author_sort | Seeber, Michele |
collection | PubMed |
description | 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, 2011 |
format | Online Article Text |
id | pubmed-3151548 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Wiley Subscription Services, Inc., A Wiley Company |
record_format | MEDLINE/PubMed |
spelling | pubmed-31515482011-08-09 Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces Seeber, Michele Felline, Angelo Raimondi, Francesco Muff, Stefanie Friedman, Ran Rao, Francesco Caflisch, Amedeo Fanelli, Francesca J Comput Chem Software News and Updates 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, 2011 Wiley Subscription Services, Inc., A Wiley Company 2011-04-30 2010-11-29 /pmc/articles/PMC3151548/ /pubmed/21387345 http://dx.doi.org/10.1002/jcc.21688 Text en Copyright © 2011 Wiley Periodicals, Inc., A Wiley Company http://creativecommons.org/licenses/by/2.5/ Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. |
spellingShingle | Software News and Updates Seeber, Michele Felline, Angelo Raimondi, Francesco Muff, Stefanie Friedman, Ran Rao, Francesco Caflisch, Amedeo Fanelli, Francesca Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces |
title | Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces |
title_full | Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces |
title_fullStr | Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces |
title_full_unstemmed | Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces |
title_short | Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces |
title_sort | wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces |
topic | Software News and Updates |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151548/ https://www.ncbi.nlm.nih.gov/pubmed/21387345 http://dx.doi.org/10.1002/jcc.21688 |
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