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CAVITY: Mapping the Druggable Binding Site

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Computer-Aided Drug Discovery

Part of the book series: Methods in Pharmacology and Toxicology ((MIPT))

Abstract

Identifying reliable binding sites based on three-dimensional structures of proteins and other macromolecules is a key step in drug discovery. A good definition of known binding site and the detection of a novel site can provide valuable information for drug design efforts. CAVITY is developed for the detection and analysis of ligand-binding site(s). It has the capability of detecting potential binding site as well as estimating both the ligandabilities and druggabilites of the detected binding sites. CAVITY has been successfully applied in many research projects as a stand-alone program or combined with other drug discovery software. In this chapter, we introduce the computational methods and protocols used in CAVITY, and use examples to further illustrate the detailed procedures of how to apply this computational software.

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Acknowledgments

This work was supported in part by the Ministry of Science and Technology of China (grant numbers: 2012AA020308, 2012AA020301) and the National Natural Science Foundation of China (grant numbers: 81273436, 91313302).

Author information

Authors and Affiliations

  1. College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China

    Yaxia Yuan & Luhua Lai

  2. Center for Quantitative Biology, Peking University, Beijing, 100871, China

    Yaxia Yuan & Jianfeng Pei

  3. Peking-Tsinghua Center for Life Sciences, AAIS, Peking University, Beijing, 100871, China

    Weilin Zhang

Authors
  1. Weilin Zhang
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  2. Yaxia Yuan
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  3. Jianfeng Pei
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  4. Luhua Lai
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Corresponding authors

Correspondence to Jianfeng Pei or Luhua Lai .

Editor information

Editors and Affiliations

  1. Chemistry Department, Southern Research Institute, Birmingham, Alabama, USA

    Wei Zhang

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© 2015 Springer Science+Business Media New York

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Zhang, W., Yuan, Y., Pei, J., Lai, L. (2015). CAVITY: Mapping the Druggable Binding Site. In: Zhang, W. (eds) Computer-Aided Drug Discovery. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. https://doi.org/10.1007/7653_2015_45

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  • DOI: https://doi.org/10.1007/7653_2015_45

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3519-2

  • Online ISBN: 978-1-4939-3521-5

  • eBook Packages: Springer Protocols

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