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Nucleic Acids Research Advance Access published online on May 5, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp287
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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3D-DART: a DNA structure modelling server

Marc van Dijk and Alexandre M. J. J. Bonvin*

Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, The Netherlands

*To whom correspondence may be addressed. Tel: +31 30 2533859; Fax: +31 30 2537623; Email: a.m.j.j.bonvin{at}uu.nl

Received January 30, 2009. Revised April 14, 2009. Accepted April 14, 2009.

There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required, for instance, to serve as templates for homology modeling, as starting structures for macro-molecular docking or as scaffold for NMR structure calculations. The conformational adaptability of DNA when binding to a protein is often an important factor and at the same time a limitation in such studies. As a response to the demand for 3D-structural models reflecting the intrinsic plasticity of DNA we present the 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool). The server provides an easy interface to a powerful collection of tools for the generation of DNA-structural models in custom conformations. The computational engine beyond the server makes use of the 3DNA software suite together with a collection of home-written python scripts. The server is freely available at http://haddock.chem.uu.nl/dna without any login requirement.


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