A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation
文献类型：期刊论文
| 作者 | Liu, Xinli1; Wang, Xicheng1; Jiang, Huangliang2,3 |
| 刊名 | JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS
 |
| 出版日期 | 2008-04-24 |
| 卷号 | 70期号:6页码:857-864 |
| 关键词 | steered molecular dynamics molecular dissociation genetic algorithm metyrapone-P450 3A4 complex |
| ISSN号 | 0165-022X |
| DOI | 10.1016/j.jbbm.2007.10.006 |
| 文献子类 | Article |
| 英文摘要 | In this paper, a steered molecular dynamics method with pulling direction optimization is proposed to dissociate ligand molecule from receptor. A multi-population genetic algorithm based on the information entropy is developed to search the optimal pulling direction. By imposing an optimization phase in the conventional steered molecular dynamics simulation, a better substrate-exit channel for the buried active site can be found. The novel simulation method has been used to dissociate the substrate-bound complex structure of cytochrome P450 3A4-metyrapone. The results show that the new pathway obtained by the proposed method has advantages such as lower energy barrier, less dissociation time and shorter motion trajectory than that by the conventional steered molecular dynamics. (c) 2007 Elsevier B.V. All rights reserved. |
| WOS关键词 | CYTOCHROME-P450 3A4 ; ACTIVE-SITE ; SIMULATION ; BINDING ; FORCE ; METYRAPONE ; PATHWAY ; ACCESS |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics |
| 语种 | 英语 |
| WOS记录号 | WOS:000256393200010 |
| 出版者 | ELSEVIER SCIENCE BV |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/272936]  |
| 专题 | 新药研究国家重点实验室 中科院受体结构与功能重点实验室 |
| 通讯作者 | Wang, Xicheng |
| 作者单位 | 1.Dalian Univ Technol, Dept Engn Mech, State Key Lab Struct Anal Ind Equipment, Dalian 116023, Liaoning, Peoples R China; 2.E China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China; 3.Chinese Acad Sci, Drug Discovery & Design Ctr,Grad Sch, State Key Lab Drug Res,Shanghai Inst Biol Sci, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Xinli,Wang, Xicheng,Jiang, Huangliang. A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation[J]. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS,2008,70(6):857-864. |
| APA | Liu, Xinli,Wang, Xicheng,&Jiang, Huangliang.(2008).A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation.JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS,70(6),857-864. |
| MLA | Liu, Xinli,et al."A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation".JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 70.6(2008):857-864. |
入库方式： OAI收割
来源：上海药物研究所
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