Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model

2019 ◽  
Vol 123 (11) ◽  
pp. 2469-2478 ◽  
Author(s):  
Duy Phuoc Tran ◽  
Akio Kitao
Keyword(s):  
Molecular Dynamics ◽  
State Model ◽  
Dissociation Process ◽  
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.

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...

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
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