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The Brownian dynamics method was used for qualitative analysis of the events that lead to the formation of a functionally active plastocyanin–cytochrome f complex. The intermediate states of this process were identified by density-based hierarchical clustering. Diffusive entrapment of plastocyanin by cytochrome f is the key point of the suggested putative scenario of protein–protein encounter. The...
The application of Brownian dynamics for simulation of transient protein–protein interactions is reviewed. The review focuses on the theoretical basics of the Brownian-dynamics method, its particular implementations, and the advantages and drawbacks of this method. The outlook for future development of Brownian dynamics-based simulation techniques is discussed. Special attention is given to analysis...
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