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Bioinformatics Advance Access published online on August 23, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm378
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* The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Wordom: a program for efficient analysis of molecular dynamics simulations

Michele Seeber *, Marco Cecchini , Francesco Rao , Giovanni Settanni and Amedeo Caflisch *

Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland

*To whom correspondence should be addressed. Amedeo Caflisch, E-mail: caflisch{at}bioc.unizh.ch


  Abstract

Summary: Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules, and efficient handling of large sets of trajectories

Availability: The Wordom program is distributed with full source code (in the C language) and documentation for usage and further development as a platform-independent package under a GPL license from http://www.biochem-caflisch.unizh.ch/wordom/

Contact: caflisch{at}bioc.unizh.ch, mseeber{at}unimore.it

Associate Editor: Prof. Alfonso Valencia

Received on May 9, 2007; revised on July 11, 2007; accepted on July 15, 2007

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