Fragment-based drug design, which utilizes computer-modeling programs to predict how small molecules bind to proteins, is becoming an increasingly widespread tool for drug discovery. In the current study, HADDOCK (High Ambiguity data-driven DOCKing) was used for fragment library docking in order to explore strategies for identifying potential binding hotspots. The fragment library consisted of sixteen small molecules of various polarities. The proteins used for fragment library docking and analysis were biotin carboxylase and beta secretase. HADDOCK successfully re-docked small molecule ligands of these proteins found in published crystal structures. Results will be presented describing the relationship between fragment-specific docking protocols and sampling of the ligand binding site.

Fragment library docking with HADDOCK: Identifying protein binding hotspots and improving site sampling

253rd National Meeting (2017)

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