3D-DART: a DNA structure modelling server

By M. V. van Dijk, Alexandre M. J. J. Bonvin. 2009

327 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance (2010, methodology): “The DNA structures in these solutions were analyzed using 3DNA (34,35) and the DNA bend analysis algorithm used in the 3D-DART server (29).”
The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study (2016, methodology): “The structure of the 12 nucleotides missing in the NMR data was added using the online tool 3D-DART [25].”
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (2019, methodology): “Other web servers for nucleic acid structures include the Curves+ web server (15) for analysis, 3DDART (16), and the ‘make-na’ server (10), built on top of NAB, for modeling (Supplemental Data S5).”
Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems (2019, methodology): “A standard B-DNA conformation built using our 3D-DART webserver 34 was the starting conformation for all protein-DNA cases.”
Structural Basis for Sequence Specific DNA Binding and Protein Dimerization of HOXA13 (2011, methodology): “The starting structure of the DNA duplex (B-form) was generated using 3D-DART [52].”