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

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

Author information

1
Department of Biological Science, Purdue University, West Lafayette, IN, USA.
2
Department of Biological Science, Purdue University, West Lafayette, IN, USA. dkihara@purdue.edu.
3
Department of Computer Science, Purdue University, West Lafayette, IN, USA. dkihara@purdue.edu.

Abstract

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 http://kiharalab.org/plps2 . 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

PMID:
29594770
DOI:
10.1007/978-1-4939-7756-7_7
[Indexed for MEDLINE]

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