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LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance

Fragment-based drug design is a popular approach in drug discovery, which makes use of computational methods such as molecular docking. To assess fragment placement performance of molecular docking programs, we constructed LEADS-FRAG, a benchmark data set containing 93 high-quality protein-fragment complexes that were selected from the Protein Data Bank using a rational and unbiased process. The data set contains fully prepared protein and fragment structures and is publicly available. Moreover, we used LEADS-FRAG for evaluating the small-molecule docking programs AutoDock, AutoDock Vina, FlexX, and GOLD for their fragment docking performance. GOLD in combination with the scoring function ChemPLP and AutoDock Vina performed best and generated near-native conformations (root mean square deviation <1.5 Å) for more than 50% of the data set considering the top-ranked docking pose. Taking into account all docking poses, the tested programs generated near-native conformations for up to 86% of the fragments in LEADS-FRAG. By rescoring all docking poses with the GOLD scoring functions and the Protein-Ligand Informatics force field, the number of near-native conformations increased up to 40% with respect to the top-rescored poses. Our results show that conventional small-molecule docking programs achieve a satisfactory fragment docking performance when utilizing rescoring.