Construction of the Markov State Model from Atomic Molecular Dynamics Simulations
6:26
Conducting Coarse-Grained Simulation to Sample Long-Time Dynamics
6:57
Results: Structure-Based Simulation and Sampling of Transcription Factor Protein Movements
8:45
Conclusion
Trascrizione
The goal of this protocol is to reveal structural dynamics of one-dimensional diffusion of protein along DNA, using a plant transcription factor WRKY domain protein as an exemplary system. The atomic simulations under the Markov state model constr
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The goal of this protocol is to reveal structural dynamics of one-dimensional diffusion of protein along DNA, using a plant transcription factor WRKY domain protein as an exemplary system. To do this, both atomistic and coarse-grained molecular dynamics simulations along with extensive computational samplings have been implemented.