3D-DART: a DNA structure modelling server

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...

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Bibliographic Details
Published in:Nucleic acids research 2009-07, Vol.37 (suppl-2), p.W235-W239
Main Authors: van Dijk, Marc, Bonvin, Alexandre M. J. J.
Format: Article
Language:English
Subjects:
DNA - chemistry
Internet
Models, Molecular
Nucleic Acid Conformation
Software
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkp287