Surflex-Dock 2.1: Robust Performance from Ligand Energetic Modeling, Ring Flexibility, and Knowledge-Based Search

Department of Biopharmaceutical Sciences, UCSF Cancer Research Institute, University of California-San Francisco, Box 0128, San Francisco, CA 94143-0128, USA.
Journal of Computer-Aided Molecular Design (Impact Factor: 2.99). 06/2007; 21(5):281-306. DOI: 10.1007/s10822-007-9114-2
Source: PubMed


The Surflex flexible molecular docking method has been generalized and extended in two primary areas related to the search component of docking. First, incorporation of a small-molecule force-field extends the search into Cartesian coordinates constrained by internal ligand energetics. Whereas previous versions searched only the alignment and acyclic torsional space of the ligand, the new approach supports dynamic ring flexibility and all-atom optimization of docked ligand poses. Second, knowledge of well established molecular interactions between ligand fragments and a target protein can be directly exploited to guide the search process. This offers advantages in some cases over the search strategy where ligand alignment is guided solely by a "protomol" (a pre-computed molecular representation of an idealized ligand). Results are presented on both docking accuracy and screening utility using multiple publicly available benchmark data sets that place Surflex's performance in the context of other molecular docking methods. In terms of docking accuracy, Surflex-Dock 2.1 performs as well as the best available methods. In the area of screening utility, Surflex's performance is extremely robust, and it is clearly superior to other methods within the set of cases for which comparative data are available, with roughly double the screening enrichment performance.

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    • "Builder and were then optimized using the Tripos force field for 2000 generations two times or more, until the minimized conformers of the ligand were the same. The flexible docking method, called Surflex-Dock [46], docks the ligand automatically into the ligand binding site of the receptor by using a protocol-based approach and an empirically derived scoring function [47]. The protocol is a computational representation of a putative ligand that binds to the intended binding site and is a unique and essential element of the docking algorithm [48]. "
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