Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein-Ligand Docking Method

Methods Mol Biol. 2018;1762:105-121. doi: 10.1007/978-1-4939-7756-7_7.


Virtual screening is a computational technique for predicting a potent binding compound for a receptor protein from a ligand library. It has been a widely used in the drug discovery field to reduce the efforts of medicinal chemists to find hit compounds by experiments.Here, we introduce our novel structure-based virtual screening program, PL-PatchSurfer, which uses molecular surface representation with the three-dimensional Zernike descriptors, which is an effective mathematical representation for identifying physicochemical complementarities between local surfaces of a target protein and a ligand. The advantage of the surface-patch description is its tolerance on a receptor and compound structure variation. PL-PatchSurfer2 achieves higher accuracy on apo form and computationally modeled receptor structures than conventional structure-based virtual screening programs. Thus, PL-PatchSurfer2 opens up an opportunity for targets that do not have their crystal structures. The program is provided as a stand-alone program at . We also provide files for two ligand libraries, ChEMBL and ZINC Drug-like.

Keywords: 3DZD; Drug discovery; Molecular surface; Protein–ligand interaction; Three-dimensional Zernike descriptor; Virtual screening.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Computational Biology / methods*
  • Drug Evaluation, Preclinical / methods*
  • Ligands
  • Models, Molecular
  • Molecular Docking Simulation
  • Protein Binding
  • Protein Conformation
  • Structure-Activity Relationship
  • Web Browser


  • Ligands