SKATE: A docking program that decouples systematic sampling from scoring

• Published in: Journal of computational chemistry Vol. 31; no. 14; pp. 2540 - 2554
• Main Authors: Feng, Jianwen A, Marshall, Garland R
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 15.11.2010; Wiley Subscription Services, Inc
• Subjects: Accuracy; Algorithms; Analytical chemistry; Binding Sites; Computational Biology - methods; consensus scoring drug discovery; Crystallography, X-Ray; Cyclin-dependent kinases; Cyclin-Dependent Kinases - metabolism; Discriminant analysis; Drug Discovery - methods; Hydrogen Bonding; Ligands; Models, Molecular; Molecular chemistry; Molecular Structure; Molecules; Rotation; Software; systematis search; T cell receptors; Thymidine Kinase - metabolism; virtual screening
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.21545

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in-house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross-docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin-dependent kinase.