Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics

doi:10.1021/acs.jpcb.2c03711

	Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics
	Gong, Shiqi 1,2,3; He, Xinheng 1,3,4; Meng, Qi 1; Ma, Zhiming 2,3; Shao, Bin 1; Wang, Tong 1; Liu, Tie-Yan 1
刊名	JOURNAL OF PHYSICAL CHEMISTRY B
	2022-11-08
页码	11
ISSN号	1520-6106
DOI	10.1021/acs.jpcb.2c03711
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研究方向	Chemistry
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000885488000001
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/60640]
专题	中国科学院数学与系统科学研究院
通讯作者	Shao, Bin; Wang, Tong
作者单位	1.Microsoft Res AI4Sci, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, 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.