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Bioinformatics Advance Access originally published online on August 16, 2005
Bioinformatics 2005 21(20):3931-3932; 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{at}oxfordjournals.org

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 1,2,*

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

*To whom correspondence should be addressed.

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 programed 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 is available at http://www.cs.bgu.ac.il/~meshi/API

Contact: keasar{at}cs.bgu.ac.il

Supplementary information: The Supplementary information includes (1) a detailed description of several key packages and classes, and (2) a brief presentation of results achieved by using the MESHI application—Beautify—in the CASP6 experiment.

Received on May 8, 2005; revised on July 25, 2005; accepted on August 12, 2005

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