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A Review on Molecular Docking

01/

INTRUDUCTION

docking is a technique which predict the prefer direction of one molecule to a second when jump to each other to form a steady compound

02/

There are 2 types of docking;

1. Rigid docking

2. Flexible docking

1. Rigid docking

Amirkia Azarbod

Sahar Farahani

MOLECULAR DOCKING APPROACHES

2. Flexible Docking

Molecular docking encompasses a range of methods to study the interaction between a ligand and a target protein. Understanding these methods can help in designing novel compounds and optimizing their binding affinity.

In molecular docking, several methods can be employed to predict the binding mode and affinity of a ligand with a target protein. Some of these methods include the Monte Carlo approach, Metropolis criterion, fragment-based method, distance geometry, matching approach, ligand fit approach, point complementarity approach, blind docking, and inverse docking.

International Research Journal of Pure & Applied Chemistry

What are some methods used in molecular docking?

03/

05/

MECHANISM OF DOCKING

APPLICATION

1. Protein structure organization

2. Search method and scoring

3. Modeling a flexible protein receptor

4. Studying interaction between molecules

5. Identifying inhibitor molecules

Docking is a valuable tool in drug design to understand the effects of ligand-protein interactions and optimize the design of new compounds.

Docking plays a crucial role in drug design by studying the interaction between a small molecule ligand and an enzyme protein. This binding communication between the ligand and protein can result in the activation or inhibition of the enzyme. Additionally, if the protein is a receptor, ligand binding can lead to agonist or antagonist effects. Docking is primarily used in the field of drug design, where it can be applied to small organic molecules commonly found in drugs.

How does docking contribute to drug design?

Major Steps Involved in Mechanics of Molecular Docking

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Step 1: Protein preparation involves...

Step 2: Active site prediction is done...

Step 3: Ligand preparation includes...

Step 4: The final step is...

the Docking process involves the following steps:

Hit identification: Utilize the flexible docking methods mentioned earlier to identify potential ligands that have a high binding affinity to the target protein.

Lead optimization: Once potential ligands have been identified, apply various optimization techniques to enhance their potency, selectivity, and drug-like properties.

Bioremediation: Explore the application of the optimized ligands in bioremediation processes for environmental cleanup.

Docking Assessment

The interdependence between sampling and scoring function affect the docking capacity in predict possible poses or binding affinities for novel compounds. Thus, an evaluation of a docking protocol is normally essential (when experimental data is available) to determine its

analytical capability. Docking measurement can be performing using different strategy

DOCKING ACCURACY

Assessing the accuracy of molecular docking

Map

PROSPECTIVE

BENCHMARKING

ENRICHMENT FACTOR

Evaluating the performance of a docking method on newly generated data

Comparing the performance of different docking methods

A measure of the ability of a docking method to distinguish true ligands from decoys

CONCULSION

CONCLUSION

remain significant challenge. Scoring function is

a fundamental component worth being further

improved upon in docking. Successful application

examples show that computational approaches

have the power to screen hits from a huge

database and design novel small molecules.

However, the realistic interactions between small

molecules and receptors are still relied on

experimental technology. Accurate as well

as low computational cost scoring functions

may bring docking application to a new stage.

New algorithm from industry and academia

are quickly incorporated into the high end

packages. It continues to extend role in exciting

new techniques such as computational

enzymology, genomics and proteomics search

engines.

Molecular docking provides an array of valuable

tools for drug design and analysis. Simple

visualization of molecules and easy access to

structural databases has become essential

components on the desktop of the medicinal

chemist. Commercial software program continue

to expand upon core user interface. The

probable docking method is done after

systematically screening of the target, ligand and

docking technique presentation. The ligand

flexibility though is almost determined and does

not generate much difficulty however protein

suppleness needs to be enhanced. Water

molecules should be incorporated to think the

hydrogen bonding with non-aqueous residue. It is

apparent from docking prose that it has attain a

good amount of adulthood and in this short

review, we have focused on types, approaches,

applications of molecular docking in concise but

secretarial for flexibility and thriving scoring

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