scholarly journals RPnet: A Reverse Projection Based Neural Network for Coarse-graining Metastable Conformational States for Protein Dynamics

2021 ◽  
Author(s):  
Hanlin Gu ◽  
Wei Wang ◽  
Siqin Cao ◽  
Ilona Christy Unarta ◽  
Yuan Yao ◽  
...  
Keyword(s):  
Neural Network ◽  
Molecular Dynamics ◽  
Protein Dynamics ◽  
Md Simulation ◽  
Coarse Graining ◽  
State Model ◽  
Conformational States ◽  
Markov State Model ◽  
Markov State

Markov State Model (MSM) is a powerful tool for modeling the long timescale dynamics based on numerous short molecular dynamics (MD) simulation trajectories, which makes it a useful tool for...

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 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 folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis

2017 ◽  
Vol 19 (18) ◽  
pp. 11249-11259 ◽  
Author(s):  
Shuangyan Zhou ◽  
Qianqian Wang ◽  
Yuwei Wang ◽  
Xiaojun Yao ◽  
Wei Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Structural Dynamics ◽  
Md Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Folding Mechanism ◽  
State Identification ◽  
Dynamics Simulations

MD simulation combined with MSM analysis was employed to investigate the structural dynamics and the folding mechanism of the key fragment 127–147 monomer of prion protein.

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