scholarly journals Structure and Dynamics Study of LeuT Using the Markov State Model and Perturbation Response Scanning Reveals Distinct Ion Induced Conformational States

2016 ◽  
Vol 120 (33) ◽  
pp. 8361-8368 ◽  
Author(s):  
Eliana K. Asciutto ◽  
Patrick C. Gedeon ◽  
Ignacio J. General ◽  
Jeffry D. Madura
Keyword(s):  
State Model ◽  
Conformational States ◽  
Markov State Model ◽  
Markov State ◽  
Structure And Dynamics

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 A Markov-State Model for the Regulation of the Sarcoplasmic Reticulum Ca2+ ATPase by Phospholamban

2014 ◽  
Vol 106 (2) ◽  
pp. 116a
Author(s):  
Peter M. Kekenes-Huskey ◽  
Andy Edwards ◽  
Johan Hake ◽  
Anouchka Michailova ◽  
James A. McCammon ◽  
...  
Keyword(s):  
Sarcoplasmic Reticulum ◽  
State Model ◽  
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

An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes

2019 ◽  
Vol 15 (10) ◽  
pp. 5689-5702 ◽  
Author(s):  
Mattia Bernetti ◽  
Matteo Masetti ◽  
Maurizio Recanatini ◽  
Rommie E. Amaro ◽  
Andrea Cavalli
Keyword(s):  
Drug Binding ◽  
State Model ◽  
Markov State Model ◽  
Markov State
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