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Protein–Ligand Blind Docking Using CB-Dock2

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Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2714))

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Abstract

Protein–ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and biological research. Recently, our new blind docking server named CB-Dock2 has been released and is currently being utilized by researchers worldwide. CB-Dock2 outperforms state-of-the-art methods due to its accuracy in binding site identification and binding pose prediction, which are enabled by its knowledge-based docking engine. This highly automated server offers interactive and intuitive input and output web interfaces, making it an efficient and user-friendly tool for the bioinformatics and cheminformatics communities. This chapter provides a brief overview of the methods, followed by a detailed guide on using the CB-Dock2 server. Additionally, we present a case study that evaluates the performance of protein–ligand blind docking using this tool.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China under Grant [81973243].

Author information

Authors and Affiliations

  1. Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China

    Yang Liu & Yang Cao

Authors
  1. Yang Liu
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  2. Yang Cao
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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, Karnataka, India

    Mohini Gore

  2. Department of Botany, Rajaram College Kolhapur, Kolhapur, Maharashtra, India

    Umesh B. Jagtap

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Liu, Y., Cao, Y. (2024). Protein–Ligand Blind Docking Using CB-Dock2. In: Gore, M., Jagtap, U.B. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 2714. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3441-7_6

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  • DOI: https://doi.org/10.1007/978-1-0716-3441-7_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3440-0

  • Online ISBN: 978-1-0716-3441-7

  • eBook Packages: Springer Protocols

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