Briinger-Brooks-Karplus

The Briinger-Brooks-Karplus (BBK) Langevin integrator [55] is one of the most popular and widely-implemented schemes. 

Briinger-Brooks-Karplus with post-step re-use of random number (BBK° )... 

For future reference, the Verlet algorithm [18] can be generalized to iticlude the friction and stochastic terms above, and is typically used in the following form described by Brooks, Briinger and Karplus, known as BBK [23, 37] ... 

Brooks III, C.L., Briinger, A.T. and Karplus, M. (1985) Active Site Dynamics in Protein Molecules A Stochastic Boundary Molecular Dynamics Approach,... 

Active site, stochastic boundary simulations (Brooks and Karplus 1983 Briinger et al. 1985 Brooks and Karplus 1989) of RNase complexed with a substrate, a cyclic phosphate intermediate and a product have been made to clarify the contribution of various amino acid residues to the enzymatic reaction (Haydock et al. 1990). The structure of the enzyme complexed with a true substrate, CpA, was built from the crystal results for the enzyme complexed with deoxy-CpA, the substrate analog, by introducing the 02 H hydroxyl group to include the deprotonated His 12, the protonated His potential was replaced by that for the neutral form His 119 was protonated in the simulations. 

Briinger A, Brooks CL, III, Karplus M (1984) Chem Phys Lett, 105 495... 

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