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Evaluation of Protein–Ligand Docking by Cyscore

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Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1762))

Abstract

Protein–ligand docking is a powerful method in drug discovery. The reliability of docking can be quantified by RMSD between a docking structure and an experimentally determined one. However, most experimentally determined structures are not available in practice. Evaluation by scoring functions is an alternative for assessing protein–ligand docking results. This chapter first provides a brief introduction to scoring methods used in docking. Then details are provided on how to use Cyscore programs. Finally it describes a case study for evaluation of protein–ligand docking.

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Acknowledgments

We gratefully thank Dr. Shuang Chen for the help with critical editing of the manuscript. The work was supported by the National Natural Science Foundation of China (#31401130 to Y.C).

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Authors and Affiliations

  1. Center of Growth, Metabolism and Aging, Key Lab of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People’s Republic of China

    Yang Cao

  2. Shanghai Center for Bioinformation Technology, Shanghai, People’s Republic of China

    Wentao Dai

  3. European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK

    Zhichao Miao

  4. Wellcome Trust Sanger Institute, Cambridge, UK

    Zhichao Miao

Authors
  1. Yang Cao
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  2. Wentao Dai
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  3. Zhichao Miao
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Corresponding author

Correspondence to Yang Cao .

Editor information

Editors and Affiliations

  1. Department of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, KA, India

    Mohini Gore

  2. Department of Biotechnology, Shivaji University, Kolhapur, MH, India

    Umesh B. Jagtap

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Cao, Y., Dai, W., Miao, Z. (2018). Evaluation of Protein–Ligand Docking by Cyscore. In: Gore, M., Jagtap, U. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 1762. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7756-7_12

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  • DOI: https://doi.org/10.1007/978-1-4939-7756-7_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7755-0

  • Online ISBN: 978-1-4939-7756-7

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