AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics
文献类型：期刊论文
| 作者 | Wang, Tong1; He, Xinheng1,2,3,4,5; Li, Mingyu1,6; Shao, Bin1; Liu, Tie-Yan1 |
| 刊名 | SCIENTIFIC DATA
 |
| 出版日期 | 2023-08-22 |
| 卷号 | 10期号:1页码:12 |
| DOI | 10.1038/s41597-023-02465-9 |
| 通讯作者 | Wang, Tong(watong@microsoft.com) ; Shao, Bin(binshao@microsoft.com) |
| 英文摘要 | Molecular dynamics (MD) simulations have revolutionized the modeling of biomolecular conformations and provided unprecedented insight into molecular interactions. Due to the prohibitive computational overheads of ab initio simulation for large biomolecules, dynamic modeling for proteins is generally constrained on force field with molecular mechanics, which suffers from low accuracy as well as ignores the electronic effects. Here, we report AIMD-Chig, an MD dataset including 2 million conformations of 166-atom protein Chignolin sampled at the density functional theory (DFT) level with 7,763,146 CPU hours. 10,000 conformations were initialized covering the whole conformational space of Chignolin, including folded, unfolded, and metastable states. Ab initio simulations were driven by M06-2X/6-31 G* with a Berendsen thermostat at 340 K. We reported coordinates, energies, and forces for each conformation. AIMD-Chig brings the DFT level conformational space exploration from small organic molecules to real-world proteins. It can serve as the benchmark for developing machine learning potentials for proteins and facilitate the exploration of protein dynamics with ab initio accuracy. |
| WOS关键词 | DENSITY-FUNCTIONAL THEORY ; FORCE-FIELDS ; BASIS-SETS ; SIMULATIONS ; MOTION ; STATES ; AMBER |
| WOS研究方向 | Science & Technology - Other Topics |
| 语种 | 英语 |
| WOS记录号 | WOS:001052837500002 |
| 出版者 | NATURE PORTFOLIO |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/307040]  |
| 专题 | 新药研究国家重点实验室 |
| 通讯作者 | Wang, Tong; Shao, Bin |
| 作者单位 | 1.Microsoft Res AI4Sci, Beijing, Peoples R China 2.Chinese Acad Sci, State Key Lab Drug Res, Shanghai, Peoples R China 3.Chinese Acad Sci, CAS Key Lab Receptor Res, Shanghai, Peoples R China 4.Chinese Acad Sci, Shanghai Inst Mat Med, Shanghai, Peoples R China 5.Univ Chinese Acad Sci, Beijing, Peoples R China 6.Shanghai Jiao Tong Univ, Sch Med, Dept Pathophysiol, Key Lab Cell Differentiat & Apoptosis Chinese Mini, Shanghai, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wang, Tong,He, Xinheng,Li, Mingyu,et al. AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics[J]. SCIENTIFIC DATA,2023,10(1):12. |
| APA | Wang, Tong,He, Xinheng,Li, Mingyu,Shao, Bin,&Liu, Tie-Yan.(2023).AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics.SCIENTIFIC DATA,10(1),12. |
| MLA | Wang, Tong,et al."AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics".SCIENTIFIC DATA 10.1(2023):12. |
入库方式： OAI收割
来源：上海药物研究所
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