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The information of how two proteins interact is embedded in the atomic details of their binding interfaces. These interactions, spatial-temporally coordinating each other as a network in a variable cytoplasmic environment, dominate almost all biological functions. A feasible and reliable computational model is highly demanded to realistically simulate these cellular processes and unravel the complexities beneath them. We therefore present a multiscale framework that integrates simulations on two different scales. The higher-resolution model incorporates structural information of proteins and energetics of their binding, while the lower-resolution model uses a highly simplified representation of proteins to capture the long-time-scale dynamics of a system with multiple proteins. Through a systematic benchmark test and two practical applications of biomolecular systems with specific cellular functions, we demonstrated …