Molecular Docking Challenges and Limitations

Molecular Docking Challenges and Limitations

Jahan B. Ghasemi, Azizeh Abdolmaleki, Fereshteh Shiri
Copyright: © 2017 |Pages: 25
DOI: 10.4018/978-1-5225-1762-7.ch030
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Abstract

Today, the development of new drugs is a challenging task of science. Researchers already applied molecular docking in the drug design field to simulate ligand- receptor interactions. Docking is a term used for computational schemes that attempt to find the “best” matching between two molecules in a complex formed from constituent molecules. It has a wide range of uses and applications in drug discovery. However, some defects still exist; the accuracy and speed of docking calculation is a challenge to explore and these methods can be enhanced as a solution to docking problem. The molecular docking problem can be defined as follows: Given the atomic coordinates of two molecules, predict their “correct” bound association. The chapter discusses common challenges critical aspects of docking method such as ligand- and receptor- conformation, flexibility and cavity detection, etc. It emphasis to the challenges and inadequacies with the theories behind as well as the examples.
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Background

Mutual molecular recognition is the initial point for approximately all processes in biological systems. Today, molecular docking as a very demanding computational and algorithmic tool plays a fundamental and advanced role in structural molecular biology and drug design. These computational tools help us for understanding molecular interactions of two molecules such as protein–protein or protein–ligand that is a key for the understanding of chemical process in diseases and other life issue occurrence. Molecular docking has a wide range of potential uses and can be applied in the following fields of drug discovery:

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    Structure–activity studies

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    Lead optimization

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    Finding potential leads by virtual screening

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    Providing binding hypotheses to ease predictions for mutagenesis studies

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    Helping x-ray crystallography in the fitting of substrates (Figure 1 shows a x-ray crystallography structure as PDB) and inhibitors to electron density

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    Chemical mechanism studies

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    Combinatorial library design

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