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Bioinformatics Advance Access published online on August 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti630
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 8, 2005
Revised July 25, 2005
Accepted August 12, 2005

Applications note

MESHI: a new library of Java classes for molecular modeling

Nir Kalisman 1, Ami Levi 1, Tetyana Maximova 1, Dan Reshef 2, Sharon Zafriri-Lynn 1, Yan Gleyzer 1, and Chen Keasar 3*

1 Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel
2 Department of Life Science, Ben-Gurion University, Beer-Sheva 84105, Israel
3 Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel; Department of Life Science, Ben-Gurion University, Beer-Sheva 84105, Israel

* To whom correspondence should be addressed.
Chen Keasar, E-mail: keasar{at}cs.bgu.ac.il


  Abstract

Summary: Adapting a modular and object-oriented approach in the design of molecular modeling packages may reduce the software development barrier between ideas and their programmed applications. Towards this goal we developed MESHI, a new, strictly object-oriented, molecular modeling suite written in Java. MESHI provides a comprehensive library of extendable classes for all the essential components of molecular modeling: molecular and geometry elements, energy functions and optimization methods.

Availability: MESHI and its related documentation are freely available at http://www.cs.bgu.ac.il/~meshi; The MESHI API can be found at http://www.cs.bgu.ac.il/~meshi/API.

Supplementary information: The supplementary information includes: 1) A detailed description of several key packages and classes. 2) A brief presentation of results achieved by the MESHI application - Beautify - in the CASP6 experiment.


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