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Can I use LigBuilder for DNA-based drug design?

April 26, 2017design DNA-Based drug ligbuilder

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Can I use LigBuilder for DNA-based drug design?

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The answer is “NO”. Although DNA-based drug design shares the same concepts with protein-based drug design, there are two reasons preventing you from directly applying LigBuilder to such a project: (1) New parameters are necessary for estimating the DNA-ligand interactions; (2) The binding site of a DNA (minor groove) is more open than a protein (usually a pocket), therefore the construction strategy may also need to be adjusted.