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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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09:17 min

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March 1st, 2022

DOI :

10.3791/63406-v

March 1st, 2022

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2,933 Views

Chao E*¹, Liqiang Dai*¹^,², Jiaqi Tian³^,⁴, Lin-Tai Da⁴, Jin Yu⁵^,⁶^,⁷

¹Beijing Computational Science Research Center, ²Shenzhen JL Computational Science and Applied Research Institute, ³School of Medical Informatics and Engineering, Xuzhou Medical University, ⁴Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, ⁵Department of Physics and Astronomy, University of California, Irvine, ⁶Department of Chemistry, University of California, Irvine, ⁷NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine

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要約

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Structure based Simulation

Transcription Factor Protein

DNA Diffusion

Markov State Model

Coarse grained Simulation

All atom MD Trajectory

Time independent Component Analysis

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