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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
Het doel van dit protocol is om de structurele dynamiek van eendimensionale diffusie van eiwit langs DNA te onthullen, met behulp van een plantaardig transcriptiefactor WRKY-domeineiwit als een voorbeeldig systeem. Om dit te doen, zijn zowel atomistische als grofkorrelige moleculaire dynamicasimulaties samen met uitgebreide computationele bemonsteringen geïmplementeerd.
