文献类型：期刊文献

英文题名：Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening

作者：Hu, Guoping[1];Kuang, Guanglin[1];Xiao, Wen[1];Li, Weihua[1];Liu, Guixia[1];Tang, Yun[1]

机构：[1]E China Univ Sci & Technol, Sch Pharm, Shanghai Key Lab New Drug Design, Shanghai 200237, Peoples R China

年份：2012

卷号：52

期号：5

起止页码：1103

外文期刊名：JOURNAL OF CHEMICAL INFORMATION AND MODELING

收录：;EI(收录号：20122215074278);WOS:【SCI-EXPANDED(收录号:WOS:000304385700003)】；

基金：The authors would like to thank Dr. Jianxin Duan of Schrodinger for critical reading of the manuscript. This work was supported by the 863 Project (Grant 2012AA020308), the National Natural Science Foundation of China (Grant 21072059), the 111 Project (Grant B07023), the Fundamental Research Funds for the Central Universities (Grant WY1113007), and the Shanghai Committee of Science and Technology (Grant 11DZ2260600).

语种：英文

摘要：Virtual screening (VS) can be accomplished in either ligand- or structure-based methods. in recent times, an increasing number of 2D fingerprint and 3D shape similarity methods have been used in ligand-based VS. To evaluate the performance of these ligand-based methods, retrospective VS was performed on a tailored directory of useful decoys (DUD). The VS performances of 14 2D fingerprints and four 3D shape similarity methods were compared. The results revealed that 2D fingerprints ECFP_2 and FCFP_4 yielded better performance than the 3D Phase Shape methods. These ligand-based methods were also compared with structure-based methods, such as Glide docking and Prime molecular mechanics generalized Born surface area rescoring, which demonstrated that both 2D fingerprint and 3D shape similarity methods could yield higher enrichment during early retrieval of active compounds. The results demonstrated the superiority of ligand-based methods over the docking-based screening in terms of both speed and hit enrichment. Therefore, considering ligand-based methods first in any VS workflow would be a wise option.