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Methods for Predicting Protein–Ligand Binding Sites

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Molecular Modeling of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1215))

Abstract

Ligand binding is required for many proteins to function properly. A large number of bioinformatics tools have been developed to predict ligand binding sites as a first step in understanding a protein’s function or to facilitate docking computations in virtual screening based drug design. The prediction usually requires only the three-dimensional structure (experimentally determined or computationally modeled) of the target protein to be searched for ligand binding site(s), and Web servers have been built, allowing the free and simple use of prediction tools. In this chapter, we review the underlying concepts of the methods used by various tools, and discuss their different features and the related issues of ligand binding site prediction. Some cautionary notes about the use of these tools are also provided.

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Authors and Affiliations

  1. Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

    Zhong-Ru Xie & Ming-Jing Hwang

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  1. Zhong-Ru Xie
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Correspondence to Ming-Jing Hwang .

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  1. University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom

    Andreas Kukol

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Xie, ZR., Hwang, MJ. (2015). Methods for Predicting Protein–Ligand Binding Sites. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_17

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  • DOI: https://doi.org/10.1007/978-1-4939-1465-4_17

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