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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W235-9. doi: 10.1093/nar/gkp287. Epub 2009 May 5.

3D-DART: a DNA structure modelling server.

Author information

1
Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, The Netherlands.

Abstract

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.

PMID:
19417072
PMCID:
PMC2703913
DOI:
10.1093/nar/gkp287
[Indexed for MEDLINE]
Free PMC Article

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