Molecular Docking Challenges and Limitations

Molecular Docking Challenges and Limitations

Jahan B. Ghasemi (University of Tehran, Iran), Azizeh Abdolmaleki (Islamic Azad University of Touyserkan, Iran) and Fereshteh Shiri (University of Zabol, Iran)
DOI: 10.4018/978-1-5225-0362-0.ch003
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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:

  • Structure–activity studies

  • Lead optimization

  • Finding potential leads by virtual screening

  • Providing binding hypotheses to ease predictions for mutagenesis studies

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

  • Chemical mechanism studies

  • Combinatorial library design

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