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Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery

  • Varun Chahal , Sonam Nirwan and Rita Kakkar EMAIL logo
Published/Copyright: August 20, 2019
Become an author with De Gruyter Brill

Abstract

With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.

Acknowledgements

The authors Varun and Sonam acknowledge financial assistance in the form of Junior Research Fellowship from Council of Scientific and Industrial Research (CSIR) and Senior Research Fellowship (SRF) from University Grants Commission (UGC), respectively.

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Published Online: 2019-08-20

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