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SAnDReS: A Computational Tool for Docking

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Docking Screens for Drug Discovery

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

Abstract

Since the early 1980s, we have witnessed considerable progress in the development and application of docking programs to assess protein–ligand interactions. Most of these applications had as a goal the identification of potential new binders to protein targets. Another remarkable progress is taking place in the determination of the structures of protein–ligand complexes, mostly using X-ray diffraction crystallography. Considering these developments, we have a favorable scenario for the creation of a computational tool that integrates into one workflow all steps involved in molecular docking simulations. We had these goals in mind when we developed the program SAnDReS. This program allows the integration of all computational features related to modern docking studies into one workflow. SAnDReS not only carries out docking simulations but also evaluates several docking protocols allowing the selection of the best approach for a given protein system. SAnDReS is a free and open-source (GNU General Public License) computational environment for running docking simulations. Here, we describe the combination of SAnDReS and AutoDock4 for protein–ligand docking simulations. AutoDock4 is a free program that has been applied to over a thousand receptor–ligand docking simulations. The dataset described in this chapter is available for downloading at https://github.com/azevedolab/sandres

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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). SAnDReS: A Computational Tool for Docking. 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_4

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  • DOI: https://doi.org/10.1007/978-1-4939-9752-7_4

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  • Publisher Name: Humana, New York, NY

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