Evaluation of Protein–Ligand Docking by Cyscore

Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Binding pocket Cyscore CurvatureSurface Protein–ligand docking Scoring function 

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Center of Growth, Metabolism and Aging, Key Lab of Bio-Resources and Eco-Environment of Ministry of Education, College of Life SciencesSichuan UniversityChengduPeople’s Republic of China
  2. 2.Shanghai Center for Bioinformation TechnologyShanghaiPeople’s Republic of China
  3. 3.European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUK
  4. 4.Wellcome Trust Sanger InstituteCambridgeUK

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