The importance of protein flexibility for accurate description of the native state has been increasingly recognized, and the success of molecular docking programs is strongly affected by protein flexibility and solvation. HADDOCK (High Ambiguity Driven DOCKing) (Dominguez et al. J. Amer. Chem. Soc. 2003) is a computational biomolecular docking approach developed to make use of available experimental and/or bioinformatics data to drive the docking process, and it allows flexibility of both ligand and protein at the biomolecular interface.  To expand the utility of HADDOCK to protein-ligand docking, ligand-specific protocols have been developed and tested.  In this study, we analyze the performance of HADDOCK on the Astex Diverse Set of protein-ligand complexes (and corresponding complexes from the Astex Non-Native Set), and an optimized procedure is presented for cases where the standard HADDOCK protocol fails.  Finally, we demonstrate the influence of available experimental NMR data on docking with a real case situation.

Information-driven fully flexible HADDOCKing: Performance on a benchmark of protein-ligand complexes

245th National Meeting (2013)

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