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Bioinformatics Advance Access published online on February 17, 2006
Bioinformatics, 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
Received December 19, 2005
Revised January 25, 2006
Accepted February 14, 2006

Applications note

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

Surjit B. Dixit 1 * and David L. Beveridge 1

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

* To whom correspondence should be addressed.
Surjit B. Dixit, E-mail: sdixit{at}wesleyan.edu


  Abstract

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 molecular dynamics simulation trajectories comprising of 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.

Associate Editor: Martin Bishop
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