Evaluation of Protein-Ligand Docking by Cyscore

Methods Mol Biol. 2018:1762:233-243. doi: 10.1007/978-1-4939-7756-7_12.

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.

Keywords: Binding pocket; CurvatureSurface; Cyscore; Protein–ligand docking; Scoring function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Computational Biology / methods*
  • Databases, Protein
  • Ligands
  • Models, Molecular
  • Molecular Docking Simulation
  • Protein Binding
  • Proteins / chemistry*
  • Software

Substances

  • Ligands
  • Proteins