Molecular Docking

Molecular Docking

Given the atomic resolution structure of a macromolecule, such as an enzyme, it should be possible to find novel molecules that bind to it, modulating its activity. Molecular docking (MD) has become an increasingly important tool for drug discovery. An increasing number of new therapeutic targets and many structural details of proteins and protein-ligand complexes allow the computational strategies to permeate all aspects of drug discovery. (Meng, Xuan-Yu, et al.). Molecular docking used to predict the intermolecular complex formed between constituent molecules (two or more) and is increasingly considered for lead discovery.

The introduction of new algorithms and programs - Along with efforts to improve established docking programs, such as AutoDock, DOCK, Ecepp/ Prodock, FlexX, FLOG, GOLD, GREEN, ICM, LUDI, Pro_LEADS, QXP and GLIDE and other new docking programs have been published in the past year, including the EUDOC algorithm SEEDS and MM ( Shoichet, Brian K., et al.). A fundamental problem with molecular docking is that orientation space is very large and grows combinatorially with the number of degrees of freedom of the interacting molecules.

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Organization and sampling techniques are available to remove the exponential time dependence on molecular size in docking calculations (Shoichet, B. K., et al.).

Glide docking:

The Glide docking hierarchy

Glide approximates a complete systematic search of the conformational, orientational and positional space of the docked ligand. While preparing Proteins using the Protein Preparation Wizard window, the first step is Review and Modify, next the Het name list clicked and deleted. In many cases want to keep specific water molecules if they are found in the binding site because they can act as a hydrogen bonding bridge between the protein and ligand otherwise can delete all water molecules.

Glide employs two forms of Glide Score: (i) Glide Score SP (Standard-Precision) (ii) Glide Score XP (Extra-Precision). These modes of actions are formulated with different objectives in mind. Distinctively, Glide Score SP is a softer function, in cases in which the Glide pose has significant imperfections. This version seeks to minimize false negatives and is appropriate for many database screening applications. In contrast, Glide Score XP is a harder function that exacts severe penalties for poses that violate established physical chemistry principles. This version of Glide Score is more adept at minimizing false positives and can be especially useful in lead optimization. (Friesner, Richard A., et al.)