期刊
JOURNAL OF CHEMICAL INFORMATION AND MODELING
卷 51, 期 9, 页码 2107-2114出版社
AMER CHEMICAL SOC
DOI: 10.1021/ci200080g
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资金
- OpenEye Scientific Software Inc. (Santa Fe, NM)
- Tripos, Inc. (St. Louis, MO)
- NIH [R21GM088517]
- NSF [0953839]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0953839] Funding Source: National Science Foundation
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 angstrom 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 (http://www.csardock.org/).
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