Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics
文献类型：期刊论文
| 作者 | Gong, Shiqi1,2,3; He, Xinheng2,3,4; Meng, Qi3; Ma, Zhiming1,2; Shao, Bin3; Wang, Tong3; Liu, Tie-Yan3 |
| 刊名 | JOURNAL OF PHYSICAL CHEMISTRY B
 |
| 出版日期 | 2022-11-08 |
| 页码 | 11 |
| ISSN号 | 1520-6106 |
| DOI | 10.1021/acs.jpcb.2c03711 |
| 通讯作者 | Shao, Bin(binshao@microsoft.com) ; Wang, Tong(watong@microsoft.com) |
| 英文摘要 | Markov state models (MSMs) play a key role in studying protein conformational dynamics. A sliding count window with a fixed lag time is widely used to sample sub-trajectories for transition counting and MSM construction. However, sub trajectories sampled with a fixed lag time may not perform well under different selections of lag time, which requires strong prior practice and leads to less robust estimation. To alleviate it, we propose a novel stochastic method from a Poisson process to generate perturbative lag time for sub-trajectory sampling and utilize it to construct a Markov chain. Comprehensive evaluations on the double-well system, WW domain, BPTI, and RBD-ACE2 complex of SARS-CoV-2 reveal that our algorithm significantly increases the robustness and power of a constructed MSM without disturbing the Markovian properties. Furthermore, the superiority of our algorithm is amplified for slow dynamic modes in complex biological processes. |
| WOS关键词 | VARIATIONAL APPROACH ; REVEAL |
| WOS研究方向 | Chemistry |
| 语种 | 英语 |
| WOS记录号 | WOS:000885488000001 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/304683]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Shao, Bin; Wang, Tong |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Microsoft Res AI4Sci, Beijing 100080, Peoples R China 4.Chinese Acad Sci, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, Shanghai 201203, Peoples R China |
| 推荐引用方式 GB/T 7714 | Gong, Shiqi,He, Xinheng,Meng, Qi,et al. Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2022:11. |
| APA | Gong, Shiqi.,He, Xinheng.,Meng, Qi.,Ma, Zhiming.,Shao, Bin.,...&Liu, Tie-Yan.(2022).Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics.JOURNAL OF PHYSICAL CHEMISTRY B,11. |
| MLA | Gong, Shiqi,et al."Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics".JOURNAL OF PHYSICAL CHEMISTRY B (2022):11. |
入库方式： OAI收割
来源：上海药物研究所
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