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Bioinformatics Advance Access published online on May 17, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm259
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

T-Pile - a package for thermodynamic calculations for biomolecules

Dominik Gront * and Andrzej Kolinski

Warsaw University, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland

*To whom correspondence should be addressed. Mr. Dominik Gront, E-mail: dgront{at}chem.uw.edu.pl


  Abstract

Summary: Molecular Dynamics and Monte Carlo, usually conducted in canonical ensemble, deliver a plethora of biomolecular conformations. Proper analysis of the simulation data is a crucial part of biophysical and bioinformatics studies. Sequence alignment problem can be also formulated in terms of Boltzmann distribution. Therefore tools for efficient analysis of canonical ensemble data become extremely valuable. T-Pile package, presented here provides a user-friendly implementation of most important algorithms such as multihistogram analysis and reweighting technique. The package can be used in studies of virtually any system governed by Boltzmann distribution.

Availability: T-Pile can be downloaded from: http://biocomp.chem.uw.edu.pl/services/tpile. These pages provide a comprehensive tutorial and documentation with illustrative examples of applications.

Associate Editor: Prof. Anna Tramontano

Received on April 13, 2007; revised on April 13, 2007; accepted on May 8, 2007

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