Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

doi:10.1021/acs.jpcb.2c03711

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	Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics
	Gong, Shiqi1,2,3 ; He, Xinheng 2,3,4; Meng, Qi 3; Ma, Zhiming1,2 ; Shao, Bin 3; Wang, Tong 3; Liu, Tie-Yan 3
	2022-11-08
发表期刊	JOURNAL OF PHYSICAL CHEMISTRY B
ISSN	1520-6106
页码	11
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.
DOI	10.1021/acs.jpcb.2c03711
收录类别	SCI
语种	英语
WOS研究方向	Chemistry
WOS类目	Chemistry, Physical
WOS记录号	WOS:000885488000001
出版者	AMER CHEMICAL SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/60641
专题	应用数学研究所
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.