Current State-of-the-art for Virtual Screening and Docking Methods - New Developments in Medicinal Chemistry - page 97

flexibility of the receptor). It combines ensemble docking to use the conformation
cluster of the receptors. Soft-docking (flexibility of a receptor is considered by
changing the repulsion term of the protein ligand interaction in scoring functions,
such as the Lennard-Jones potential term) is used to set the coefficient for every
atom of the receptor and to relax the collisions between protein and ligand atoms.
Evaluation of the ligand-binding mode can be made by the GENIUS Score. After
a number of iteration steps it yields the predicted protein-ligand complex [514].
BetaDock approach solves the docking problem by putting the priority on shape
complementarity between a receptor and a ligand whereas the approach is based
on the theory of the β-complex. From the Voronoi diagram of the receptor (with
topology stored in the quasi-triangulation) the β-complex corresponding to water
molecule can be computed. The β-shape with the complete proximity information
among all atoms on the receptor boundary is defined by the boundary of the β-
complex. Pockets are computed where ligands may bind from the β-shape. The
ligand quickly placed within each pocket by solving the singular value
decomposition problem and the assignment problem. Taking as initial solutions
the conformations of ligands within the pockets, genetic algorithms are used to
find the optimal solution for the docking problem [515].
ParaDockS is a framework for molecular docking with population-based
metaheuristics. The approach is the combination of an optimization algorithm and
an objective function that describes the interaction. The software is designed to
hold different optimization algorithms and objective functions. An adapted
particle-swarm optimizer is implemented and the objective functions are the
empirical p-Score and knowledge-based potentials [516].
DockoMatic is a high throughput inverse virtual screening and homology
modeling tool (free and open source application) that unifies a suite of software
programs within a user-friendly graphical user interface (GUI) to facilitate
molecular docking experiments. Users can efficiently setup, start and manage IVS
experiments through the GUI by specifying receptors, ligands, grid parameters
and docking engine. This yields automatically the required experiment input files
and output directories. The user can manage and monitor job progress and a
summary of results is generated upon job completion [517].