Evaluation of Protein–Ligand Docking by Cyscore
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 wordsBinding pocket Cyscore CurvatureSurface Protein–ligand docking Scoring function
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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