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      Weighted-ensemble Brownian dynamics simulations for protein association reactions

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      Biophysical Journal
      Elsevier BV

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          Abstract

          A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation of protein-association reactions and other events whose frequencies of outcomes are constricted by free energy barriers. The method features a weighted ensemble of trajectories in configuration space with energy levels dictating the proper correspondence between "particles" and probability. Instead of waiting a very long time for an unlikely event to occur, the probability packets are split, and small packets of probability are allowed to diffuse almost immediately into regions of configuration space that are less likely to be sampled. The method has been applied to the Northrup and Erickson (1992) model of docking-type diffusion-limited reactions and yields reaction rate constants in agreement with those obtained by direct Brownian simulation, but at a fraction of the CPU time (10(-4) to 10(-3), depending on the model). Because the method is essentially a variant of standard Brownian dynamics algorithms, it is anticipated that weighted-ensemble Brownian dynamics, in conjunction with biophysical force models, can be applied to a large class of association reactions of interest to the biophysics community.

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          Author and article information

          Journal
          Biophysical Journal
          Biophysical Journal
          Elsevier BV
          00063495
          January 1996
          January 1996
          : 70
          : 1
          : 97-110
          Article
          10.1016/S0006-3495(96)79552-8
          1224912
          8770190
          a8a14f51-7f9e-41d3-bc0a-2a8817229115
          © 1996

          https://www.elsevier.com/tdm/userlicense/1.0/

          https://www.elsevier.com/open-access/userlicense/1.0/

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