With many docking programs designed to model protein-protein interactions, HADDOCK sets itself apart by allowing for protein flexibility and utilizing diverse types of experimental and bioinformatics data to drive the docking.  The program has recently been used to model protein-ligand interactions using the Astex Diverse Set.  In this study, HADDOCK standard and solvated protocols were compared for published test complexes with water-mediated protein-ligand interactions.  Additionally, the influence of protein starting conformation on docking success was tested, using representative complexes from the Astex Non-Native Set.  Success rates are presented for both sampling and scoring of solvated and standard protocols, using various input protein conformations.

Benchmarking the HADDOCK solvated protocol for protein-ligand docking

247th National Meeting (2014)

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