Kinetic parameters are important factors for determining the efficacy of potential drugs. However, traditional simulation techniques are unable to access the timescales needed to observe multiple association or dissociation events, and therefore cannot accurately estimate kinetic rates. We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open source scripts and tools that facilitate the calculation of kinetic rates using a multiscale, hybrid, molecular dynamics, Brownian dynamics and milestoning approach. We also present the calculation of kinetic rates for the well-studied protein trypsin with its competitive inhibitor benzamidine to demonstrate the accuracy and efficiency of the SEEKR package.<br/>

Multiscale estimation of kinetic rates of trypsin with benzamidine using a hybrid molecular dynamics, brownian dynamics, and milestoning approach

253rd National Meeting (2017)

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