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How Docking Programs Work

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Docking Screens for Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2053))

Abstract

Protein–ligand docking simulations are of central interest for computer-aided drug design. Docking is also of pivotal importance to understand the structural basis for protein–ligand binding affinity. In the last decades, we have seen an explosion in the number of three-dimensional structures of protein–ligand complexes available at the Protein Data Bank. These structures gave further support for the development and validation of in silico approaches to address the binding of small molecules to proteins. As a result, we have now dozens of open source programs and web servers to carry out molecular docking simulations. The development of the docking programs and the success of such simulations called the attention of a broad spectrum of researchers not necessarily familiar with computer simulations. In this scenario, it is essential for those involved in experimental studies of protein–ligand interactions and biophysical techniques to have a glimpse of the basics of the protein–ligand docking simulations. Applications of protein–ligand docking simulations to drug development and discovery were able to identify hits, inhibitors, and even drugs. In the present chapter, we cover the fundamental ideas behind protein–ligand docking programs for non-specialists, which may benefit from such knowledge when studying molecular recognition mechanism.

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Acknowledgments

This work was supported by grants from CNPq (Brazil) (308883/2014-4). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior—Brasil (CAPES)—Finance Code 001. GB-F acknowledges support from PUCRS/BPA fellowship. WFA is a senior researcher for CNPq (Brazil) (Process Numbers: 308883/2014-4 and 309029/2018-0).

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  1. Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul—PUCRS, Porto Alegre, RS, Brazil

    Gabriela Bitencourt-Ferreira & Walter Filgueira de Azevedo Jr.

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  1. Gabriela Bitencourt-Ferreira
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  2. Walter Filgueira de Azevedo Jr.
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Correspondence to Walter Filgueira de Azevedo Jr. .

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  1. Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul—PUCRS, Porto Alegre, Rio Grande do Sul, Brazil

    Walter Filgueira de Azevedo Jr.

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Bitencourt-Ferreira, G., de Azevedo, W.F. (2019). How Docking Programs Work. In: de Azevedo Jr., W. (eds) Docking Screens for Drug Discovery. Methods in Molecular Biology, vol 2053. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9752-7_3

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  • DOI: https://doi.org/10.1007/978-1-4939-9752-7_3

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  • Publisher Name: Humana, New York, NY

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  • Online ISBN: 978-1-4939-9752-7

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