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Biology
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基于结构的转录因子蛋白沿DNA从原子级步进到粗晶扩散运动的模拟和采样
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Biology
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JoVE Journal
Biology
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Please note that all translations are automatically generated.
Click here for the English version.
基于结构的转录因子蛋白沿DNA从原子级步进到粗晶扩散运动的模拟和采样
DOI:
10.3791/63406-v
•
09:17 min
•
March 01, 2022
•
Chao E*
1
,
Liqiang Dai*
1,2
,
Jiaqi Tian
4
,
Lin-Tai Da
,
Jin Yu
6,7
1
Beijing Computational Science Research Center
,
2
Shenzhen JL Computational Science and Applied Research Institute
,
3
School of Medical Informatics and Engineering
,
Xuzhou Medical University
,
4
Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine
,
Shanghai Jiao Tong University
,
5
Department of Physics and Astronomy
,
University of California, Irvine
,
6
Department of Chemistry
,
University of California, Irvine
,
7
NSF-Simons Center for Multiscale Cell Fate Research
,
University of California, Irvine
Chapters
00:04
Introduction
00:45
Construction of the Markov State Model from Atomic Molecular Dynamics Simulations
06:26
Conducting Coarse-Grained Simulation to Sample Long-Time Dynamics
06:57
Results: Structure-Based Simulation and Sampling of Transcription Factor Protein Movements
08:45
Conclusion
Summary
Automatic Translation
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Automatic Translation
该协议的目标是揭示蛋白质沿DNA的一维扩散的结构动力学,使用植物转录因子WRKY结构域蛋白作为示例系统。为此,已经实施了原子和粗粒度分子动力学模拟以及广泛的计算采样。
Tags
Structure-based Simulation
Transcription Factor Protein
DNA Diffusion
Markov State Model
Coarse-grained Simulation
All-atom MD Trajectory
VMD
RMSD
Rotational Degree
K-means Clustering
Atomistic System
GROMACS
Time-independent Component Analysis
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