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

Molecules

Woong-Hee Shin²  Xiaolei Zhu³  Mark Gregory Bures¹  Daisuke Kihara² 

[1] Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, IN 46285, USA; E-Mail:;Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA; E-Mail:;School of Life Science, Anhui University, Hefei 230601, China; E-Mail:

关键词: ligand-based virtual screening;    three-dimensional similarity;    ROCS;    USR;    3D Zernike descriptors;    Patch-Surfer;    PL-PatchSurfer;    molecular shape;    molecular surface;   

DOI  :  10.3390/molecules200712841

来源: mdpi

【 摘 要 】

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), two-dimensional (2D), and three-dimensional (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 were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability to find dissimilar active compounds, and computational speed.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.