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| - Rapid Estimation of Relative Protein−Ligand Binding Affinities Using aHigh-Throughput Version of MM-PBSA
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| - By employing a modified protocol of the Molecular Mechanics with Poisson−Boltzmann Surface Area(MM-PBSA) methodology we substantially decrease the required computation time for calculating relativeestimates of protein−ligand binding affinities. The modified method uses a generalized Born implicit solvationmodel during molecular dynamics to enhance conformational sampling as well as a very efficient Poisson−Boltzmann solver and a computational design based on a distributed-computing paradigm. This constructionallows for reduction of the computational cost of the calculations by roughly 2 orders of magnitude comparedto the traditional formulation of MM-PBSA. With this high-throughput version of MM-PBSA we show thatone can produce efficient physics-based estimates of relative binding free energies with reasonable correlationto experimental data and a total computation time that is sufficiently low such that an industrially relevantthroughput can be realized given currently accessible computing resources. We demonstrate this approachby performing a comparison of different MM-PBSA implementations on a set of 18 ligands for the proteintarget urokinase.
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