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Basic Theory of Molecular Docking

Molecular Docking is a computational method used to predict interactions between molecular structures. It involves sampling and scoring algorithms to determine the best binding poses of ligands with target proteins. Various types of docking protocols exist, including rigid, flexible, and blind docking, and several tools are required for the process, such as AutoDock and PyMol.

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76 views8 pages

Basic Theory of Molecular Docking

Molecular Docking is a computational method used to predict interactions between molecular structures. It involves sampling and scoring algorithms to determine the best binding poses of ligands with target proteins. Various types of docking protocols exist, including rigid, flexible, and blind docking, and several tools are required for the process, such as AutoDock and PyMol.

Uploaded by

dton9816
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

BASIC THEORY OF MOLECULAR

DOCKING
What is Molecular Docking ?
Molecular Docking is a computational method, it is used to predict
how two or more molecular structures interacts with each other.
Algorithm

Sampling algorithm Scoring algorithm

A sampling algorithm is used to


The scoring algorithm is used to
predict how many possible
calculate the binding energies of each
confirmations the ligand can assume
pose with the target protein.
to bind with the target protein.

POSE: The binding confirmation of ligand with protein is known as pose.

A pose with the lowest energy is considered as best pose.


Shape
Matching
Algorithm

Genetic Incremental
Constructio
Algorithm n Algorithm

Sampling
algorithm
Multiple
Monte Copy
Carlo Simulation
Search

LUDI
Force Field
Algorithm

Consensus-
Empirical
based Scoring Scoring
Scoring Algorithms Function
Function

Knowledge
-based
Scoring
Function
Types of Molecular Docking

Docking Protocol
Rigid Docking
Specific Docking

Constrained Docking
Blind Docking
Flexible Docking
Molecular Docking Steps

Selection of Preparation Selection and Setting


Defining
Protein 3D of Protein Preparation parameters Analysis
Active Site
Structure structure of Ligand for Docking
Requirement for Molecular Docking
Modeller

ChemDraw

Open Babel GUI


Protein MGL Tools

AutoDock

AutoDock Vina
Ligand
PyMol

Discovery Studio
Computational
Tools RCSB PDB

PubChem

ZINC Database

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