Chapter title |
Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein–Ligand Docking Method
|
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Chapter number | 7 |
Book title |
Computational Drug Discovery and Design
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Published in |
Methods in molecular biology, January 2018
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DOI | 10.1007/978-1-4939-7756-7_7 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7755-0, 978-1-4939-7756-7
|
Authors |
Woong-Hee Shin, Daisuke Kihara, Shin, Woong-Hee, Kihara, Daisuke |
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. |
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