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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
Chapters
- 00:04Introduction
- 00:45Construction of the Markov State Model from Atomic Molecular Dynamics Simulations
- 06:26Conducting Coarse-Grained Simulation to Sample Long-Time Dynamics
- 06:57Results: Structure-Based Simulation and Sampling of Transcription Factor Protein Movements
- 08:45Conclusion
Bu protokolün amacı, örnek bir sistem olarak bir bitki transkripsiyon faktörü WRKY alan proteini kullanarak, DNA boyunca proteinin tek boyutlu difüzyonunun yapısal dinamiklerini ortaya çıkarmaktır. Bunu yapmak için, hem atomistik hem de kaba taneli moleküler dinamik simülasyonları ve kapsamlı hesaplamalı örneklemeler uygulanmıştır.
