scholarly journals Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit

2017 ◽  
Vol 121 (22) ◽  
pp. 5509-5514 ◽  
Author(s):  
Kelly M. Thayer ◽  
Bharat Lakhani ◽  
David L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
State Model ◽  
Induced Fit ◽  
Conformational Selection ◽  
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 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

Exploring the folding process of human βB2-crystallin using multiscale molecular dynamics and the Markov state model

2020 ◽  
Vol 22 (46) ◽  
pp. 26753-26763
Author(s):  
José-Luis Velasco-Bolom ◽  
Laura Domínguez
Keyword(s):  
Molecular Dynamics ◽  
State Model ◽  
Protein Conformations ◽  
Folding Process ◽  
Markov State Model ◽  
Markov State ◽  
Adequate Knowledge

Adequate knowledge of protein conformations is crucial for understanding their function and their association properties with other proteins.

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.

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