An unconventional ligand‐binding mechanism of substrate‐binding proteins: MD simulation and Markov state model analysis of BtuF

2019 ◽  
Vol 40 (14) ◽  
pp. 1440-1448 ◽  
Author(s):  
Dongdong Wang ◽  
Jingwei Weng ◽  
Wenning Wang
Keyword(s):  
Ligand Binding ◽  
Md Simulation ◽  
Binding Proteins ◽  
Substrate Binding ◽  
Model Analysis ◽  
State Model ◽  
Binding Mechanism ◽  
Markov State Model ◽  
Markov State

scholarly journals Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

2014 ◽  
Vol 10 (8) ◽  
pp. e1003767 ◽  
Author(s):  
Shuo Gu ◽  
Daniel-Adriano Silva ◽  
Luming Meng ◽  
Alexander Yue ◽  
Xuhui Huang
Keyword(s):  
Ligand Binding ◽  
Binding Protein ◽  
Model Analysis ◽  
State Model ◽  
Markov State Model ◽  
Markov State ◽  
Binding Mechanisms

To probe the binding pathway of a selective compound (D089-0563) to c-MYC Pu24 G-quadruplex using free ligand binding simulations and Markov state model analysis

2020 ◽  
Vol 22 (39) ◽  
pp. 22567-22583
Author(s):  
Brian Chen ◽  
Griffin Fountain ◽  
Holli-Joi Sullivan ◽  
Nicholas Paradis ◽  
Chun Wu
Keyword(s):  
Ligand Binding ◽  
Promoter Region ◽  
Free Ligand ◽  
State Model ◽  
Binding Mechanism ◽  
Myc Oncogene ◽  
Markov State Model ◽  
Markov State ◽  
Anti Cancer ◽  
G Quadruplex

D089-0563 is a highly promising anti-cancer compound that selectively binds the transcription-silencing G-quadruplex element (Pu27) at the promoter region of the human c-MYC oncogene; however, its binding mechanism remains elusive.

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

Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis

2021 ◽  
Vol 17 (4) ◽  
pp. 2022-2033
Author(s):  
François Sicard ◽  
Vladimir Koskin ◽  
Alessia Annibale ◽  
Edina Rosta
Keyword(s):  
Model Analysis ◽  
State Model ◽  
Markov State Model ◽  
Markov State

scholarly journals Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis

2021 ◽  
pp. 2102435
Author(s):  
Xueping Hu ◽  
Jinping Pang ◽  
Jintu Zhang ◽  
Chao Shen ◽  
Xin Chai ◽  
...  
Keyword(s):  
Md Simulations ◽  
Model Analysis ◽  
State Model ◽  
Markov State Model ◽  
Markov State

Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis

2020 ◽  
Vol 142 (51) ◽  
pp. 21344-21352
Author(s):  
Jingwei Weng ◽  
Maohua Yang ◽  
Wenning Wang ◽  
Xin Xu ◽  
Zhongqun Tian
Keyword(s):  
Self Assembly ◽  
Model Analysis ◽  
State Model ◽  
Markov State Model ◽  
Thermodynamics And Kinetics ◽  
Markov State ◽  
Kinetics Of
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