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Many computational methods have become standard techniques in modern drug discovery. However, approaches which employ explicit molecular dynamics simulations still are restricted to special applications, as their extensive computational requirements make it difficult to obtain results within the necessary time scale of industrial drug development projects. Moreover, a high expertise is needed to analyze...
Factor Xa (fXa) is a promising target for antithrombotic drugs. Recently, we presented a molecular dynamics study on fXa, which highlighted the need for a careful system setup to obtain stable simulations. Here, we show that these simulations can be used to predict the free energy of binding of several fXa inhibitors. We tested molecular mechanics/Poisson–Boltzmann surface area, molecular mechanics/Generalized...
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