1. M.V.Lomonosov Moscow State University, Department of Chemistry, Physical Chemistry Division, Laboratory of Chemical Cybernetics
Section: Experimental/Clinical Study
Year: 2004
A new version of the hybrid quantum mechanical – molecular mechanical (QM/MM) method for modeling chemical reactions in protein environments is developed and implemented as a computer program. The method is based on the effective fragment potential technique and assumes partitioning of the MM subsystem into flexible chains of effective fragments interacting with the quantum subsystem and between themselves. The computer program of the QM/MM method allows one to locate stationary points on complex multidimensional potential surfaces for the systems composed of several hundreds atoms. The applications include the reaction of hydrolysis of peptide bonds catalyzed by serine proteases, the reactions of proton transfer along oriented hydrogen bonding networks
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Nemukhin A.V., Grigorenko B.L., Epifanovsky E.M., Rogov A.V. (2004) Modeling mechanisms of enzymatic reactions by the hybrid quantum mechanical – molecular mechanical methods. Biomeditsinskaya Khimiya, 50(application 1), 49-55.
Nemukhin A.V. et al. Modeling mechanisms of enzymatic reactions by the hybrid quantum mechanical – molecular mechanical methods // Biomeditsinskaya Khimiya. - 2004. - V. 50. -N application 1. - P. 49-55.
Nemukhin A.V. et al., "Modeling mechanisms of enzymatic reactions by the hybrid quantum mechanical – molecular mechanical methods." Biomeditsinskaya Khimiya 50.application 1 (2004): 49-55.
Nemukhin, A. V., Grigorenko, B. L., Epifanovsky, E. M., Rogov, A. V. (2004). Modeling mechanisms of enzymatic reactions by the hybrid quantum mechanical – molecular mechanical methods. Biomeditsinskaya Khimiya, 50(application 1), 49-55.
