A worldwide e-Infrastructure for NMR and structural biology

Getting started with 3D-DART

There is a growing interest in the structural study of DNA in complex with a ligand or in their native form. Experimental techniques such as Nuclear Magnetic Resonance spectroscopy (NMR) and X-ray crystallography as well as computational methods try to gain more insight into the structure and function of these molecules.

An important part in the pipeline of DNA structural studies is the generation of models. Often, 3D structural models of DNA are required, for instance, to serve as templates for homology modelling, as starting structures for macro-molecular docking or as a scaffold for NMR structure calculations. An example for the use of DNA models in a computational method is the generation of starting structures for a molecular docking run performed by HADDOCK.

The intrinsic flexibility of DNA is often an important factor and at the same time limitation in such studies. DNA flexibility is observed both at a "local" level in the orientation of one Watson-Crick partner and at a "global" level as bends and kinks in the overall structure.
The 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool) provides a convenient means of generating custom 3D structural models of DNA with control over the local and global conformation.
3D-DART uses the DNA rebuild functionality of the well-known software package 3DNA Lu et al. and extends its functionally with tools to change the global conformation of the DNA models.

We developed 3D-DART to be of general use in the generation of nucleic acid structure models. 3D-DART is free and open to all users and there is no login requirement. We welcome all suggestions aimed at improving or expanding the capabilities of the tools and the web site.

The 3D-DART server allows you to generated 3D structural models of DNA from a sequence a base-pair step parameter file or another DNA starting structure. You can manipulate the conformation of the DNA structure using the following structural parameters:

  • Nucleic acid type (A-DNA, B-DNA)
  • Global and local bend-angle
  • Orientation of the bend-angle in Euler-angle space
  • Location of the bend-angle in the sequence
  • Custom values for base-pair and base-pair step parameters

Additional features include the output of 3D structures and associated restraint files for use in the macro-molecular docking program HADDOCK  and the generation of Calladine-Drew plots for illustrative or educational purposes.

If you use 3D-DART please cite:

  • M. van Dijk and A.M.J.J. Bonvin (2009) "3D-DART: a DNA structure modelling server", Nucl. Acids Res., 37 (Web Server Issue):W235-W239 doi:10.1093/nar/gkp287

Start using the 3D-DART web server

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life