Simulation-Enabled Estimation of Kinetic Rates (SEEKR) is a scientific software package used to calculate the probabilities and timescales of ligand-receptor binding by combining the results of both molecular dynamics (MD) and Brownian dynamics (BD) with the theory of milestoning. MD is a relatively accurate simulation technique, however it is also time-consuming to adequately sample biomolecular motion, such as binding events. In contrast, BD very quickly simulates molecular binding events, but lacks the accuracy of MD when the molecules are in close contact. In order to reduce the computational cost of running binding simulations, SEEKR uses MD to simulate the molecules when they are close together, but otherwise uses BD for large intermolecular distances. Milestoning is then used to combine the results of BD and MD. SEEKR utilizes the OpenMM MD simulation program, which leverages the power of the graphical processing unit (GPU) on desktop computers. This enables us to obtain thermodynamics and kinetics data that can be obtain within a timescale similar to the time it would take to perform the same task on a supercomputer, but is far cheaper and more accessible. To ensure the validity of the method, SEEKR was tested on the insulin-phenol system to better understand the binding process of the system as well as demonstrate the utility of SEEKR. This approach allows us to gain biological insight using the simulations to compute thermodynamics and kinetics data on intermolecular binding at an efficient computational cost.

Using the SEEKR program to gain biological insight into the insulin-phenol system

Macromolecular Chemistry: The Second Century

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