Fig. 6. Binding kinetics in the MSM.

a On-rate k_on, off-rate k_off, and dissociation constant K_d of ubiquitin and SH3c calculated from the MSM for the state threshold value $p_{\mathrm{bind}}^{*}=0.57$ at which the experimental value for K_d is obtained. Unbound/bound states of the MSM are defined as states with $p_{\mathrm{bind}}^{*}$ values smaller/larger than the state threshold value. Super and sub-scripts indicate a 95% confidence interval of the posterior distribution of the MSM transition matrix. b K_d, k_on, and k_off, as a function of the state threshold value $p_{\mathrm{bind}}^{*}$. The threshold $p_{\mathrm{bind}}^{*}=0.57$ in (a) is located within a plausible transition state region. However, the entire range of predicted K_d values for different threshold choices is within the expected error of current state-of-the-art force field. The rates in subscript and superscript in (a) and the error regions in (b) represent 95% confidence intervals of the posterior distribution of Markov models.