%0 Journal Article %1 Rojnuckarin2000WEBReaction %A Rojnuckarin, Atipat %A Livesay, Dennis R. %A Subramaniam, Shankar %D 2000 %J Biophysical Journal %K brownian-dynamics reaction-simulations weighted-ensemble %N 2 %P 686 - 693 %R http://dx.doi.org/10.1016/S0006-3495(00)76327-2 %T Bimolecular Reaction Simulation Using Weighted Ensemble Brownian Dynamics and the University of Houston Brownian Dynamics Program %U http://www.sciencedirect.com/science/article/pii/S0006349500763272 %V 79 %X 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.

@article{Rojnuckarin2000WEBReaction, abstract = {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. }, added-at = {2016-05-20T19:36:17.000+0200}, author = {Rojnuckarin, Atipat and Livesay, Dennis R. and Subramaniam, Shankar}, biburl = {https://www.bibsonomy.org/bibtex/2f8c0d6c5196ee8ecb633d87212e91852/salotz}, description = {Bimolecular Reaction Simulation Using Weighted Ensemble Brownian Dynamics and the University of Houston Brownian Dynamics Program}, doi = {http://dx.doi.org/10.1016/S0006-3495(00)76327-2}, interhash = {2ba22267d43cc9954ce4f97dfb264e03}, intrahash = {f8c0d6c5196ee8ecb633d87212e91852}, issn = {0006-3495}, journal = {Biophysical Journal }, keywords = {brownian-dynamics reaction-simulations weighted-ensemble}, number = 2, pages = {686 - 693}, timestamp = {2016-05-20T19:36:17.000+0200}, title = {Bimolecular Reaction Simulation Using Weighted Ensemble Brownian Dynamics and the University of Houston Brownian Dynamics Program }, url = {http://www.sciencedirect.com/science/article/pii/S0006349500763272}, volume = 79, year = 2000 }