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Building Machine-Learning Scoring Functions for Structure-Based Prediction of Intermolecular Binding Affinity

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Docking Screens for Drug Discovery

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

Abstract

Molecular docking enables large-scale prediction of whether and how small molecules bind to a macromolecular target. Machine-learning scoring functions are particularly well suited to predict the strength of this interaction. Here we describe how to build RF-Score, a scoring function utilizing the machine-learning technique known as Random Forest (RF). We also point out how to use different data, features, and regression models using either R or Python programming languages.

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Acknowledgments

This work was supported by INSERM and the Polish Ministry of Science and Higher Education POIG.02.02.00-14-024/08-00 and POIG.02.03.00-00-003/09-00.

Author information

Authors and Affiliations

  1. Institute of Biochemistry and Biophysics PAS, Warsaw, Poland

    Maciej Wójcikowski & Pawel Siedlecki

  2. Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Poland

    Pawel Siedlecki

  3. Cancer Research Center of Marseille, INSERM U1068, Marseille, France

    Pedro J. Ballester

  4. Institut Paoli-Calmettes, Marseille, France

    Pedro J. Ballester

  5. Aix-Marseille Université, Marseille, France

    Pedro J. Ballester

  6. CNRS UMR7258, Marseille, France

    Pedro J. Ballester

Authors
  1. Maciej Wójcikowski
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  2. Pawel Siedlecki
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  3. Pedro J. Ballester
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Corresponding author

Correspondence to Pedro J. Ballester .

Editor information

Editors and Affiliations

  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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Wójcikowski, M., Siedlecki, P., Ballester, P.J. (2019). Building Machine-Learning Scoring Functions for Structure-Based Prediction of Intermolecular Binding Affinity. 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_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9752-7_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9751-0

  • Online ISBN: 978-1-4939-9752-7

  • eBook Packages: Springer Protocols

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