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Biophys J, August 2000, p. 686-693, Vol. 79, No. 2

Bimolecular Reaction Simulation Using Weighted Ensemble Brownian Dynamics and the University of Houston Brownian Dynamics Program

Atipat Rojnuckarin,* Dennis R. Livesay,dagger Dagger § and Shankar SubramaniamDagger §

 *Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706;  dagger Department of Chemistry and  Dagger National Center for Supercomputing Applications, University of Illinois, Illinois 61820; and  §Departments of Biochemistry, Chemical Engineering, Electrical and Computer Engineering, and Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, University of Illinois, Illinois 61820 USA

We discuss here the implementation of the Weighted Ensemble Brownian (WEB) dynamics algorithm of Huber and Kim in the University of Houston Brownian Dynamics (UHBD) suite of programs and its application to bimolecular association problems. WEB dynamics is a biased Brownian dynamics (BD) algorithm that is more efficient than the standard Northrup-Allison-McCammon (NAM) method in cases where reaction events are infrequent because of intervening free energy barriers. Test cases reported here include the Smoluchowski rate for association of spheres, the association of the enzyme copper-zinc superoxide dismutase with superoxide anion, and the binding of the superpotent sweetener N-(p-cyanophenyl)-N'-(diphenylmethyl)-guanidinium acetic acid to a monoclonal antibody fragment, NC6.8. Our results show that the WEB dynamics algorithm is a superior simulation method for enzyme-substrate reaction encounters with large free energy barriers.

Biophys J, August 2000, p. 686-693, Vol. 79, No. 2
© 2000 by the Biophysical Society   0006-3495/00/08/686/08  $2.00


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