scholarly journals A new class of enhanced kinetic sampling methods for building Markov state models

2017 ◽  
Vol 147 (15) ◽  
pp. 152702 ◽  
Author(s):  
Arti Bhoutekar ◽  
Susmita Ghosh ◽  
Swati Bhattacharya ◽  
Abhijit Chatterjee
Keyword(s):  
Sampling Methods ◽  
New Class ◽  
Markov State ◽  
Markov State Models ◽  
State Models

scholarly journals Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

2021 ◽  
Author(s):  
Arghadwip Paul ◽  
Suman Samantray ◽  
Marco Anteghini ◽  
Mohammed Khaled ◽  
Birgit Strodel
Keyword(s):  
Amyloid Β ◽  
Md Simulations ◽  
Amyloid Β Peptide ◽  
Intrinsically Disordered ◽  
Thermodynamics And Kinetics ◽  
Markov State ◽  
Markov State Models ◽  
State Models ◽  
Kinetics Of

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.

scholarly journals Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

2015 ◽  
Vol 11 (7) ◽  
pp. e1004404 ◽  
Author(s):  
Hanlun Jiang ◽  
Fu Kit Sheong ◽  
Lizhe Zhu ◽  
Xin Gao ◽  
Julie Bernauer ◽  
...  
Keyword(s):  
Argonaute Protein ◽  
Selective Binding ◽  
Markov State ◽  
Markov State Models ◽  
State Models ◽  
Step Mechanism

scholarly journals Markov state models based on milestoning

2011 ◽  
Vol 134 (20) ◽  
pp. 204105 ◽  
Author(s):  
Christof Schütte ◽  
Frank Noé ◽  
Jianfeng Lu ◽  
Marco Sarich ◽  
Eric Vanden-Eijnden
Keyword(s):  
Markov State ◽  
Markov State Models ◽  
State Models
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