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In this work, the authors developed a new method for determination of binding areas in proteins and precomplex structure with allowance for the Brownian diffusion and electrostatic interactions of proteins that occur when proteins approach one another. This method significantly simplies subsequent precise simulation and prediction of the final complex structure. The Brownian dynamics method, which can be used for predicting the structure of protein complexes, considers the interaction of only two molecules in solution. A characteristic feature and novelty of the method, as is shown below, is the possibility to use it for studying interaction of several protein molecules simultaneously. This makes it possible to simulate the formation of a large number of complexes, which takes place in solution or cell compartments and to monitor the real-time kinetics of this process.