Supercomputer Docking

Alexey V. Sulimov, Danil C. Kutov, Vladimir B. Sulimov

Abstract


This review is based on the peer–reviewed research literature including the author’s own publications devoted to supercomputer docking. The general view on docking and its role at the initial stage of the rational drug design is presented. Molecules of medicine compounds selectively bind to the active site of a protein, which is responsible for the disease progression, and stop it. Docking programs perform positioning of molecules (ligands) in the active site of the protein and estimate the protein–ligand binding energy. The larger this energy is, the less concentration of the respective compound should be used to observe the desired effect. Several classical docking programs are described in short. Examples of the adaptation of existing docking programs to supercomputing and using them for virtual screening of millions of ligands are presented. Two novel generalized docking programs specially designed for multi–core docking of a single ligand on a supercomputer are described shortly. These programs find a sufficiently wide spectrum of low energy minima of a protein–ligand complex in the frame of a given force field. The quasi–docking procedure using the generalized docking program is described. Quasi–docking allows to perform docking with quantum–chemical semiempirical methods. Finally a summary is made based on the materials presented.


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References


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