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Introduction to Molecular Docking

Introduction to Molecular Docking

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Published by achsanuddin
a very brief and general overview of molecular docking concept
a very brief and general overview of molecular docking concept

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Published by: achsanuddin on Dec 13, 2008
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04/05/2013

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Introduction to Molecular Docking
 
(a very brief and general overview)
 © 
Achsanuddin 12 Dec 08
 
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.
Objectives.
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)
Introduction.
 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
 
Molecular surface of a proteinPrediction of the binding affinity will be useful when you are synthesizing compoundswhereby you can predict the affinity of your desired compound towards a certain target (say aprotein or DNA; with particular interest to stop the function of the enzyme/protein or to blockcertain reaction).You can therefore save a lot time and money by “experimenting” using the computer firstbefore actually going to the lab to make your compound. In addition, you can predict how amolecule interact or react with another molecule for example in protein – protein interaction, in aspecific biological reaction (of your interest) before conducting the (“wet”) experiment.This method is also useful when you want to screen (they call it “virtual screening”) anumber of compounds say from a natural product or plants/herbs to see whether your smallmolecules (from the medicinal plants/herbs) will have certain pharmacological effects on aparticular protein or enzyme (for example HIV protease etc.). Large pharmaceutical companiesin Europe and US have been using this technique for some time in the discovery anddevelopment of new drugs.There are two main types of docking (molecular docking) in practice: small molecule – protein (called “ligand – protein docking”) and protein – protein docking. As mentioned earlier,there is also small molecule – DNA or RNA docking done by some researchers. I believe, thiscan be categorized as ligand – DNA/RNA docking.Protein – protein docking involves two protein molecules simulated by thecomputer/computer program to bind/interact with one another. However, in this case, theinteractions are basically rigid compared to the ligand – protein docking. You might be able tosee that by simulating certain protein – protein interactions in a specific biological reaction, youcan get some information or insights at the molecular level on how a certain mechanism tookplace.
 © 
Achsanuddin 12 Dec 08

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