We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. To demonstrate its utility, we compute the kon, koff, and ΔGbind for the protein trypsin with its noncovalent binder, benzamidine, and examine the kinetics and other results generated in the context of the new software, and compare our findings to previous studies performed on the same system. We compute a kon estimate of (2.1 ± 0.3) × 10(7) M(-1) s(-1), a koff estimate of 83 ± 14 s(-1), and a ΔGbind of -7.4 ± 0.1 kcal·mol(-1), all of which compare closely to the experimentally measured values of 2.9 × 10(7) M(-1) s(-1), 600 ± 300 s(-1), and -6.71 ± 0.05 kcal·mol(-1), respectively.
This work describes an example of using Milestoning in kinetic calculations.
The following methods are also used: