Molecular Docking: A Review Paper

Authors

  • Namrata Arya Assistant Professor, School of Applied Sciences, Sanskriti University, Mathura, Uttar Pradesh Author
  • Arminder Kaur Assistant Professor, School of Applied Sciences, Sanskriti University, Mathura, Uttar Pradesh Author

Keywords:

Docking, Ligand, Molecular, Models, Orientation

Abstract

 Molecular docking basically explains about  the orientation of a molecule preferred to the other  molecule in a manner as in when they attach to each other  in order to get a steady complex. By using scoring functions  further the power of alliance or the irrevocable affinity of  the different molecules is predicted by the preferred  orientation of the two molecules. These interactions, which are achieved by molecular docking between important  biological components such as proteins, peptides, nucleic  acid, carbohydrates, and lipids, are crucial in signal  transduction. Further, these interactions between two  molecules which are being performed by the help of  molecular docking also helps in predicting the type of  signals produced. Therefore, molecular docking is helpful  in predicting both strength and type of signals produced by  the molecules. Because of its ability to predict the coupling  compliance of small particle ligands to the appropriate  target restriction site, molecular docking is among the most  often used strategies in structure-based drug design.  Characterization of the coupling conduct assumes a  significant job in discerning structure of medications just as  to clarify crucial biochemical procedures. 

Downloads

Download data is not yet available.

References

O. Roche, R. Kiyama, and C. L. Brooks, “Ligand-protein database: Linking protein-ligand complex structures to binding data,” J. Med. Chem., 2001, doi: 10.1021/jm000467k.

L. Hu, M. L. Benson, R. D. Smith, M. G. Lerner, and H. A. Carlson, “Binding MOAD (Mother of All Databases),” Proteins Struct. Funct. Genet., 2005, doi: 10.1002/prot.20512.

J. J. Irwin and B. K. Shoichet, “ZINC - A free database of commercially available compounds for virtual screening,” J. Chem. Inf. Model., 2005, doi: 10.1021/ci049714+.

H. M. Berman et al., “The Protein Data Bank,” Nucleic Acids Research. 2000, doi: 10.1093/nar/28.1.235.

A. Pozzan, “Molecular Descriptors and Methods for Ligand Based Virtual High Throughput Screening in Drug Discovery,” Curr. Pharm. Des., 2006, doi: 10.2174/138161206777585247.

P. C. D. Hawkins, A. G. Skillman, and A. Nicholls, “Comparison of shape-matching and docking as virtual screening tools,” J. Med. Chem., 2007, doi: 10.1021/jm0603365.

S. F. Sousa, P. A. Fernandes, and M. J. Ramos, “Protein ligand docking: Current status and future challenges,” Proteins: Structure, Function and Genetics. 2006, doi: 10.1002/prot.21082.

G. M. Morris et al., “Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function,” J. Comput. Chem., 1998, doi: 10.1002/(SICI)1096- 987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B.

G. M. Morris, D. S. Goodsell, R. Huey, and A. J. Olson, “Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4,” J. Comput. Aided. Mol. Des., 1996, doi: 10.1007/BF00124499.

D. S. Goodsell and A. J. Olson, “Automated docking of substrates to proteins by simulated annealing,” Proteins Struct. Funct. Bioinforma., 1990, doi: 10.1002/prot.340080302.

M. Hendlich, “Databases for protein-ligand complexes,” 1998, doi: 10.1107/S0907444998007124.

Downloads

Published

2023-10-28

How to Cite

Molecular Docking: A Review Paper . (2023). International Journal of Innovative Research in Engineering & Management, 9(1), 140–146. Retrieved from https://acspublisher.com/journals/index.php/ijirem/article/view/11253