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THE PHARMA REVIEW (JANUARY - FEBRUARY 2011)

Molecular Docking Softwares: An Overview

Laxmi Tripathi, Praveen Kumar, Jamshed Haneef, Ranjit Singh

Abstract: Molecular Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Two approaches are particularly popular within the molecular docking community. One approach uses a matching technique that describes the protein and the ligand as complementary surfaces. The second approach simulates the actual docking process in which the ligand-protein pairwise interaction energies are calculated. There are three types of Docking: Protien-Protien Docking, Protien-Ligand Docking and Protien-Protien & Protien-Ligand docking. Softwares used in protein-protein docking include Affinity, Autodock, Combibuild, Dockvision, Fred, Flexidock, Flex-X, Glide, Gold, Ligplot, Situs And Vega. Softwares used in protein-ligand docking include Dock, Gramm, ICM-Dock and Patch Dock. Softwares used in Protien-Protien & Protien-Ligand docking include 3d-Dock Suite, Bielefeld Protein Docking, Bigger, Cluspro, Dot (Daughter Of Turnip), Haddock And Hex. The present review compiles the characteristics and applications of the different softwares used in docking studies.
Introduction
Molecular Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules. Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Given the biological and pharmaceutical significance of molecular docking, considerable efforts have been directed towards improving the methods used to predict docking.
Molecular docking may be defined as an optimization process, which would describe the "best-fit" orientation of a ligand that binds to a particular protein of interest. However since both the ligand and the protein are flexible, a "hand-in-glove" analogy is more appropriate than "lock-and-key". During the course of the process, the ligand and the protein adjust their conformation to achieve an overall "best-fit" and this kind of conformational adjustments resulting in the overall binding is referred to as "induced-fit". The focus of molecular docking is to computationally stimulate the molecular recognition process. The aim of molecular docking is to achieve an optimized conformation for both the protein and ligand and relative orientation between protein and ligand such that the free energy of the overall system is minimized.

 

 

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