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Bioinformatics Advance Access originally published online on February 17, 2006
Bioinformatics 2006 22(8):1007-1009; doi:10.1093/bioinformatics/btl059
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Surjit B. Dixit * and David L. Beveridge

Department of Chemistry and Molecular Biophysics Program Hall-Atwater Laboratories, Wesleyan University Middletown CT 06459, USA

*To whom correspondence should be addressed.

Summary: We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. The backend of this interface is a relational database storing the conformational details of DNA obtained in 39 different MD simulation trajectories comprising all the 136 unique tetranucleotide steps. Examples of the use of this data to predict DNA structures are included.

Availability: http://humphry.chem.wesleyan.edu:8080/MDDNA

Contact: sdixit{at}wesleyan.edu

Supplementary information: Supplementary data including color figures are available at Bioinformatics online.

Received on December 19, 2005; revised on January 25, 2006; accepted on February 14, 2006

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