An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy
文献类型：期刊论文
| 作者 | Bai, Fang1,2; Liao, Sha3; Gu, Junfeng1; Jiang, Hualiang4 ; Wang, Xicheng1; Li, Honglin3
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| 刊名 | JOURNAL OF CHEMICAL INFORMATION AND MODELING
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| 出版日期 | 2015-04 |
| 卷号 | 55期号:4页码:833-847 |
| ISSN号 | 1549-9596 |
| DOI | 10.1021/ci500647f |
| 文献子类 | Article |
| 英文摘要 | Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, miiltiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloproteinspecific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDock(Zn), an extensive comparison was performed against six universal, popular docking programs: Glide XP mbde, Glide SP mode, Gold, Auto Dock, AutoDock4(zn), and EADock DSS, The zinc metalloprotein-specific knoWledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDock(Zn) had a competitive ability to sample and identify native binding poses With a higher success rate than the other six docking programs. |
| WOS关键词 | PROTEIN-LIGAND INTERACTIONS ; FORCE-FIELD ; ACCESSIBLE DATABASE ; BINDING AFFINITIES ; PDBBIND DATABASE ; DATA-BANK ; COMPLEXES ; PREDICTION ; INHIBITORS ; ENERGIES |
| 资助项目 | 863 Hi-Tech Program of China[2012AA020308] ; National Natural Science Foundation of China[81222046] ; National Natural Science Foundation of China[81230076] ; National Natural Science Foundation of China[11202049] ; National Natural Science Foundation of China[11072048] ; Fundamental Research Funds for the Central Universities[00000000] ; Shanghai Rising-Star Tracking Program[13QH1401100] ; Innovation Program of the Shanghai Municipal Education Commission[13SG32] ; Fok Ying Tung Education Foundation[141035] |
| WOS研究方向 | Pharmacology & Pharmacy ; Chemistry ; Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000353668600013 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/276578]  |
| 专题 | 药物发现与设计中心 中科院受体结构与功能重点实验室 新药研究国家重点实验室 |
| 通讯作者 | Li, Honglin |
| 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.Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 USA; 3.E China Univ Sci & Technol, Sch Pharm, State Key Lab Bioreactor Engn, Shanghai Key Lab New Drug Design, Shanghai 200237, Peoples R China; 4.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China |
| 推荐引用方式 GB/T 7714 | Bai, Fang,Liao, Sha,Gu, Junfeng,et al. An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2015,55(4):833-847. |
| APA | Bai, Fang,Liao, Sha,Gu, Junfeng,Jiang, Hualiang,Wang, Xicheng,&Li, Honglin.(2015).An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy.JOURNAL OF CHEMICAL INFORMATION AND MODELING,55(4),833-847. |
| MLA | Bai, Fang,et al."An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy".JOURNAL OF CHEMICAL INFORMATION AND MODELING 55.4(2015):833-847. |
入库方式： OAI收割
来源：上海药物研究所
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