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J Chem Inf Model. 2011 Sep 26;51(9):2107-14. doi: 10.1021/ci200080g. Epub 2011 Aug 3.

Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction.

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Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States.


Two sets of ligand binding decoys have been constructed for the community structure-activity resource (CSAR) benchmark by using the MDock and DOCK programs for rigid- and flexible-ligand docking, respectively. The decoys generated for each complex in the benchmark thoroughly cover the binding site and also contain a certain number of near-native binding modes. A few scoring functions have been evaluated using the ligand binding decoy sets for their abilities of predicting near-native binding modes. Among them, ITScore achieved a success rate of 86.7% for the rigid-ligand decoys and 79.7% for the flexible-ligand decoys, under the common definition of a successful prediction as root-mean-square deviation <2.0 Å from the native structure if the top-scored binding mode was considered. The decoy sets may serve as benchmarks for binding mode prediction of a scoring function, which are available at the CSAR Web site (

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