An optimization algorithm for conformer generation based on the bond contribution ranking

作者全名："Zhang, Ziheng; Zhang, Kai; Liu, Zhihui; Zhao, Jialei; Wang, Jing; Dang, Yongjun; Hu, Junchi"

作者地址："[Zhang, Ziheng] Chongqing Med Univ, Sch Lab Med, Chongqing, Peoples R China; [Zhang, Kai; Dang, Yongjun; Hu, Junchi] Chongqing Med Univ, Inst Life Sci, Ctr Novel Target & Therapeut Intervent, Chongqing, Peoples R China; [Liu, Zhihui; Zhao, Jialei; Wang, Jing] Chongqing Med Univ, Clin Coll 1, Chongqing, Peoples R China; [Wang, Jing] Fudan Univ, Jinshan Hosp, Dept Orthopaed, Shanghai, Peoples R China; [Hu, Junchi] Chinese Acad Sci, Shanghai Inst Mat Med, Ctr Chem Biol, Drug Discovery & Design Ctr,State Key Lab Drug Res, Shanghai, Peoples R China"

通信作者："Dang, YJ; Hu, JC (通讯作者)，Chongqing Med Univ, Inst Life Sci, Ctr Novel Target & Therapeut Intervent, Chongqing, Peoples R China."

来源：COMPUTATIONAL BIOLOGY AND CHEMISTRY

ESI学科分类：COMPUTER SCIENCE

WOS号：WOS:000863052700004

JCR分区：Q2

影响因子：3.1

年份：2022

卷号：100

期号：　

开始页：　

结束页：　

文献类型：Article

关键词：Conformer generation; Bond contribution rank; Systematic sampling; Torsion angle

摘要："Many works in computational drug discovery require the conformer generation of small molecules. Most existing tools aim to generate diverse conformers and deal with all of the rotatable bonds without distinction. There are some problems in existing approaches, such as the combinatorial explosion of conformers along with the number of rotatable bonds increasing and the incomplete sampling of the conformational space. Here, we present an optimized conformer generation algorithm based on the bond contribution ranking (ABCR) to find the optimal conformer under any specified scoring function. Compared with existing methods, our method can improve molecular conformational searching and protein-ligand docking performance. Meanwhile, our method has the same or broader coverage of conformational space in the global conformer sampling. Our research shows it can achieve the optima with small numbers of generated conformers and small numbers of iterations."

基金机构："Natural Science Foundation of Chongqing, China [cstc2021jcyj-msxmX0311]; SKY Project, Chongqing Medical University, Chongqing, China [202010]"

基金资助正文："This work was supported by Natural Science Foundation of Chongqing, China (cstc2021jcyj-msxmX0311) ; and SKY Project, Chongqing Medical University, Chongqing, China (202010) ."