Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations

2016 ◽  
Vol 56 (6) ◽  
pp. 1205-1215 ◽  
Author(s):  
Yan Li ◽  
Zigang Dong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Clustering Algorithm ◽  
State Model ◽  
Markov State Model ◽  
Markov State ◽  
Dynamics Simulations

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.

The Synergistic Mechanism of Apo-Ferritin Structural Transitions and Au(III) ions Transportation: A Molecular Dynamics Simulations with Markov State Model

2021 ◽  
Author(s):  
Xue Peng ◽  
Chenlin Lu ◽  
Zheng Liu ◽  
Diannan Lu
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Transport Mechanism ◽  
Markov State Model ◽  
Markov State ◽  
Unique Structure ◽  
Synergistic Mechanism ◽  
Nanomaterials Synthesis ◽  
Dynamics Simulations

Due to its unique structure, recent years witness the use of apo-ferritin to accumulate various non-natural metal ions as a scaffold for nanomaterials synthesis. However, the transport mechanism of metal...

Kinetics of CO2 diffusion in human carbonic anhydrase: a study using molecular dynamics simulations and the Markov-state model

2017 ◽  
Vol 19 (18) ◽  
pp. 11690-11697 ◽  
Author(s):  
Gong Chen ◽  
Xian Kong ◽  
Diannan Lu ◽  
Jianzhong Wu ◽  
Zheng Liu
Keyword(s):  
Molecular Dynamics ◽  
Carbonic Anhydrase ◽  
Md Simulations ◽  
State Model ◽  
Markov State Model ◽  
Markov State ◽  
Co2 Diffusion ◽  
Human Carbonic Anhydrase ◽  
Dynamics Simulations ◽  
Kinetics Of

Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization.

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
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