Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery

Woong-Hee Shin, Xiaolei Zhu, Mark Bures, Daisuke Kihara
2015 Molecules  
Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known active ligand. Two notable advantages of LBVS methods are that they do not require structural information of a target receptor and that they are faster than structure-based methods. LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D), twodimensional (2D), and
more » ... nal (3D). Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed. In addition, four representative 3D methods of were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability of finding dissimilar active compounds, and computational speed. Keywords Ligand-based virtual screening; Three-dimensional similarity; ROCS; USR; 3D Zernike descriptors; Patch-Surfer; PL-PatchSurfer; molecular shape; molecular surface licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license
doi:10.3390/molecules200712841 pmid:26193243 pmcid:PMC5005041 fatcat:ajzknqtl3jewfmxammsgr6ylhy