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.
CITATION STYLE
Shin, W. H., & Kihara, D. (2018). Virtual ligand screening using PL-PatchSurfer2, a molecular surface-based protein–ligand docking method. In Methods in Molecular Biology (Vol. 1762, pp. 105–121). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7756-7_7
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