Molecular Docking

BioCodeKb - Bioinformatics Knowledgebase

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. Molecular docking generates different possible adduct structures that are ranked and grouped together using scoring function in the software. There are many databases available, which offer information on small ligand molecules such as CSD (Cambridge Structural Database), ACD (Available Chemical Directory), MDDR (MDL Drug Data Report) and NCI (National Cancer Institute Database). While performing docking, different interacted conformers are generated and compared with each other.

Approaches of Molecular Docking

For performing molecular docking, primarily two types of approaches are used.

Simulation approach

The ligand and target is being separated by physical distance and then ligand is allowed to bind into groove of target after “definite times of moves” in its conformational space. The moves involve variations to the structure of ligand either internally (torsional angle rotations) or externally (rotations and translations). The ligand in every move in the conformational limit releases energy, as “Total Energy”.

Shape complementarity approach

This approach employs ligand and target as surface structural feature that provides their molecular interaction. The complementarity between two surfaces based on shape matching illustration helps in searching the complementary groove for ligand on target surface.

Docking is most commonly used in the field of drug design, most drugs are small organic molecules, and docking may be applied to:

  • Hit identification: docking combined with a scoring function can be used to quickly screen large databases of potential drugs in silico to identify molecules that are likely to bind to protein target of interest

  • Lead optimization: docking can be used to predict in where and in which relative orientation a ligand binds to a molecule

  • Bioremediation: Protein ligand docking can also be used to predict pollutants that can be degraded by enzymes


  • Click Docking

  • AutoDock

  • Modeller

  • AutoDock Vina

  • DOCK

  • GOLD

  • Glide

BioinfoLytics Company

Our company BioinfoLytics is affliated with BioCode and is a project, where we are providing many topics on Genomics, Proteomics, their analysis using many tools in a better and advance way, Sequence Alignment & Analysis, Bioinformatics Scripting & Software Development, Phylogenetic and Phylogenomic Analysis, Functional Analysis, Biological Data Analysis & Visualization, Custom Analysis, Biological Database Analysis, Molecular Docking, Protein Structure Prediction and Molecular Dynamics etc. for the seekers of Biocode to further develop their interest to take part in these services to fulfill their requirements and obtain their desired results. We are providing such a platform where one can find opportunity to learn, research projects analysis and get help and huge knowledge based on molecular, computational and analytical biology.

We are providing “Molecular Docking” service to the bioinformatics community through our expertise using bioinformatics tools to study of how two or more molecular structures (e.g., drug and enzyme or protein) fit together that paves way in drug designing.

Need to learn more about Molecular Docking and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

Get in touch with us

Tel: +92 314 7785980


  • Black Instagram Icon
  • Facebook

© Copyright 2020 BioCode Ltd. - All rights reserved.