Mechanism of the All-α to All-β Conformational Transition of RfaH-CTD: Molecular Dynamics Simulation and Markov State Model

2014 ◽  
Vol 10 (6) ◽  
pp. 2255-2264 ◽  
Author(s):  
Shanshan Li ◽  
Bing Xiong ◽  
Yuan Xu ◽  
Tao Lu ◽  
Xiaomin Luo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Conformational Transition ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State

scholarly journals Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiaojun Zeng ◽  
Liyun Zhang ◽  
Xiuchan Xiao ◽  
Yuanyuan Jiang ◽  
Yanzhi Guo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State

scholarly journals Molecular Dynamics Simulation and Markov State Model Reveal Irregular Metastable Conformation and Allostery In DNAJB-PKAc

2016 ◽  
Vol 110 (3) ◽  
pp. 51a-52a
Author(s):  
Yingjie Wang ◽  
Alessandro Cembran ◽  
Jiali Gao ◽  
Gianluigi Veglia ◽  
Susan S. Taylor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State

The misfolding mechanism of the key fragment R3 of tau protein: a combined molecular dynamics simulation and Markov state model study

2020 ◽  
Vol 22 (19) ◽  
pp. 10968-10980 ◽  
Author(s):  
Hongli Liu ◽  
Haiyang Zhong ◽  
Zerong Xu ◽  
Qianqian Zhang ◽  
Syed Jawad Ali Shah ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Tau Protein ◽  
Md Simulation ◽  
Structural Characteristics ◽  
Protein A ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Model Study

All-atom molecular dynamics (MD) simulation combined with Markov state model (MSM) were used to uncover the structural characteristics and misfolding mechanism of the key R3 fragment of tau protein at the atomic level.

scholarly journals The GPCR Opsin Translocates Lipids via a Dynamic Mechanism Specified by Markov State Model Analysis of Molecular Dynamics Trajectories

2018 ◽  
Vol 114 (3) ◽  
pp. 274a
Author(s):  
Giulia Morra ◽  
Asghar M. Razavi ◽  
Kalpana Pandey ◽  
Harel Weinstein ◽  
Anant K. Menon ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Model Analysis ◽  
Dynamic Mechanism ◽  
State Model ◽  
Markov State Model ◽  
Markov State

scholarly journals Correction: Probing intrinsic dynamics and conformational transition of HIV gp120 by molecular dynamics simulation

RSC Advances ◽  
2020 ◽  
Vol 10 (61) ◽  
pp. 36988-36988
Author(s):  
Yi Li ◽  
Xiao-Ling Zhang ◽  
Xue Yuan ◽  
Jiang-Chun Hou ◽  
Peng Sang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Conformational Transition ◽  
Dynamics Simulation ◽  
Hiv Gp120

Correction for ‘Probing intrinsic dynamics and conformational transition of HIV gp120 by molecular dynamics simulation’ by Yi Li et al., RSC Adv., 2020, 10, 30499–30507, DOI: 10.1039/d0ra06416e.

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