An optimization algorithm for conformer generation based on the bond contribution ranking
文献类型：期刊论文
| 作者 | Zhang, Ziheng1; Zhang, Kai2; Liu, Zhihui3; Zhao, Jialei3; Wang, Jing3,4; Dang, Yongjun2; Hu, Junchi2,5 |
| 刊名 | COMPUTATIONAL BIOLOGY AND CHEMISTRY
 |
| 出版日期 | 2022-10 |
| 卷号 | 100页码:107751 |
| ISSN号 | 1476-9271 |
| 关键词 | Conformer generation Bond contribution rank Systematic sampling Torsion angle |
| DOI | 10.1016/j.compbiolchem.2022.107751 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| WOS关键词 | CONFORMATIONAL-ANALYSIS ; ACCURATE DOCKING ; PROTEIN ; DATABASE ; SEARCH ; GLIDE |
| WOS研究方向 | Life Sciences & Biomedicine - Other Topics ; Computer Science |
| 语种 | 英语 |
| 出版者 | ELSEVIER SCI LTD |
| WOS记录号 | WOS:000863052700004 |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/309310]  |
| 专题 | 新药研究国家重点实验室 |
| 通讯作者 | Dang, Yongjun; Hu, Junchi |
| 作者单位 | 1.Chongqing Med Univ, Sch Lab Med, Chongqing, Peoples R China; 2.Chongqing Med Univ, Inst Life Sci, Ctr Novel Target & Therapeut Intervent, Chongqing, Peoples R China; 3.Chongqing Med Univ, Clin Coll 1, Chongqing, Peoples R China; 4.Fudan Univ, Jinshan Hosp, Dept Orthopaed, Shanghai, Peoples R China; 5.Chinese Acad Sci, Shanghai Inst Mat Med, Ctr Chem Biol, Drug Discovery & Design Ctr,State Key Lab Drug Res, Shanghai, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Ziheng,Zhang, Kai,Liu, Zhihui,et al. An optimization algorithm for conformer generation based on the bond contribution ranking[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2022,100:107751. |
| APA | Zhang, Ziheng.,Zhang, Kai.,Liu, Zhihui.,Zhao, Jialei.,Wang, Jing.,...&Hu, Junchi.(2022).An optimization algorithm for conformer generation based on the bond contribution ranking.COMPUTATIONAL BIOLOGY AND CHEMISTRY,100,107751. |
| MLA | Zhang, Ziheng,et al."An optimization algorithm for conformer generation based on the bond contribution ranking".COMPUTATIONAL BIOLOGY AND CHEMISTRY 100(2022):107751. |
入库方式： OAI收割
来源：上海药物研究所
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