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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