Current State-of-the-art for Virtual Screening and Docking Methods - New Developments in Medicinal Chemistry - page 96

SKATE is a docking prototype that decouples systematic sampling from scoring
in order to improve docking accuracy. It systematically samples a ligand's
conformation, rotational and translational degrees of freedom, as constrained by a
receptor pocket, to find steric 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 [510].
CRDOCK is an ultrafast docking and virtual screening program that contains a
search engine that can use a variety of sampling methods and an initial energy
evaluation function. It uses several energy minimization algorithms for fine-
tuning the binding poses. Different scoring functions ensures the easy
configuration of custom-made protocols optimized depending on the problem at
hand. A pre computed library of ligand conformations is used. It is initially
generated from one-dimensional SMILES strings [511].
LigenDock is the docking module of Ligen which is based on two programs, i.e. a
docking program called LigenDock based on pharmacophore models of binding
sites, including a non-enumeraive docking algorithm. The accompanying module
LiGenPocket is aimed at the binding site analysis and structure-based
pharmacophere definition [512].
FIREDOCK is an efficient method for refinement and rescoring of rigid-body
docking solutions whereas the refinement process consists of two main steps. In
the first step there is rearrangement of the interface side-chains and adjustment of
the relative orientation of the molecules. The method accounts for the observation
that most interface residues that are important in recognition and binding do not
change their conformation significantly upon complexation. The second stage
involves side-chain movements, which are restricted, and thus manage to reduce
the false-positive rate noticeable. In the later stages of the procedure there is
smoothing of the atomic radii allowing for minor backbone and side-chain
movements increasing the sensitivity of the algorithm [513].
GENIUS docking system enables induced fit docking (changes both
conformation of the ligand and coordinates of the receptor to consider the