The Molecular Docking Method Essay

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In silico methods became widely used in the fields of structural molecular biology and structure-based drug design with the rapid increase in computational power. Molecular docking [2–4] is one of these in silico techniques.
Docking is a method which predicts preferred orientation (on the basis of binding energy) of one molecule to the second to form a stable complex. In the field of drug design, first molecule is usually protein/enzyme/DNA and the second one is small organic molecule/small peptides as potential drug candidate.
Knowledge of preferred orientation of ligand and protein used to predict binding affinity and to discriminate high-affinity drug candidates from the low-affinity compounds. 2.6.1Lock and key analogy
Molecular docking is sometimes described as a problem of lock and key, where one is interested in finding the correct orientation of a key (ligand) that will open the lock (protein). Although this analogy is simple to understand but it does not account for inherent flexibility of proteins and ligands which is why more appropriate term hand-in-glove is used sometimes.
2.6.2 Rigid-body docking vs. flexible docking
The docking problem involves many degrees of freedom [18]. There are three translational and three rotational degrees of freedom for each molecule as well as the conformational degrees of freedom for both molecules. The simplest approach to docking is to take into account only translational and rotational degrees of freedom and treat both receptor…