Introduction to Molecular Docking
This text is meant to give the reader a general overview of molecular docking concept. Abasic understanding of molecular docking will be presented to the reader in the simplest andeasiest manner possible. I would like to remind the readers though, that this text will not be ableto replace any kinds of textbook in particular molecular modelling or equivalent to it. Thereaders are advised to refer to those textbook pertaining to those topics for more in-depthknowledge.
This text will basically covers the following objectives:1. Definition of molecular docking (what it's all about)2. The importance of docking3. Approaches to docking (Methodologies)4. Mechanistic of docking (How to perform docking)5. Application of docking (Where it is being used)
Molecular docking is a method to predict the preferred orientation of one molecule to asecond when bound to each other to form a stable complex. Computers and programs(softwares) are used to predict or simulate the possible reaction (and interactions) between twomolecules based on their 3 dimensional structures.Using softwares, the interactions can be viewed and analyzed to understand andanswers some biological important questions regarding a certain chemical or biologicalreaction.Analyzing the interactions basically comes with (nice) 3 D graphics which can bemanipulated in several ways to clearly explore in detail (in atomic resolutions) the interactioninvolved between the atoms in the two interacting molecules.This method can therefore be used not only to predict possible binders or inhibitors, butalso to predict how strong the association between the molecules (called the binding affinity)can be. It is useful to know the binding strength (binding energy) when you are comparing(ranking) a group of compounds or derivatives to determine which derivative is the best binderor inhibitor (how strong a compound will bind to the target).
Achsanuddin 12 Dec 08