Location of the bend-angle in the sequence.Orientation of the bend-angle in Euler-angle space.You can manipulate the conformation of the DNA structure using the following structural parameters: The custom build tool allows you to generated 3D structural models of DNA from a sequence a base-pair step parameter file or another DNA starting Window once you submitted the web form you will be shortly prompted with the download location of your data. The 3D-DART web server Click on the custom build logo to bring up the web form and start modelling. Bonvin (2009) "3D-DART: a DNA structure modelling server", Nucl.
We welcome all suggestions aimed at improving or expanding the capabilities of the tools and the web site. We developed 3D-DART to be of general use in the generation of nucleic acid structure models. With tools to change the global conformation of the DNA models. With control over the local and global conformation.ģD-DART uses the DNA rebuild functionality of the well-known software package 3DNA Lu et al. The 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool) provides a convenient means of generating custom 3D structural models of DNA Observed both at a "local" level in the orientation of one Watson-Crick partner and at a "global" level as bends and kinks An example for the use of DNA models in a computational method is the generation of starting structuresįor a molecular docking run performed by HADDOCK a biomolecular docking program developed in our group The intrinsic flexibility of DNA is often an important factor and at the same time limitation in such studies. Often, 3D structural models of DNAĪre required, for instance, to serve as templates for homology modelling, as starting structures for macro-molecular docking or as a scaffoldįor NMR structure calculations.
An important part in the pipeline of DNA structural studies is the generation of models. Experimental techniques such as Nuclear Magnetic Resonance spectroscopy (NMR) and X-rayĬrystallography as well as computational methods try to gain more insight into the structure and function of these molecules. There is a growing interest in the structural study of DNA inĬomplex with a ligand or in their native form.
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