Modern drug design strategies often focus on optimization of thermodynamic parameters. However, the incorporation of kinetic data has been shown to increase the success of drug screens. Molecular dynamics (MD) offers a means of estimating these rates, but brute force simulations can be costly. SEEKR (Simulation Enhanced Estimation of Kinetic Rates), a hybrid combining MD and Brownian dynamics (BD) with milestoning, employs many short simulations to improve both efficiency and accuracy. To demonstrate the accuracy of SEEKR, we present the association and dissociation rate calculations for β-cyclodextrin, an experimentally and computationally well-studied host-guest system, with a selection of potential ligands. <br/>

Estimating kinetic rates for β-cyclodextrin

253rd National Meeting (2017)

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