> > Without having actually read their paper... there's could easily be a kind > of apples-and-oranges comparison going on. The local optimum resulting from > a single EM using MM forcefields optimized for non-vacuum conditions on > near-native folds in vacuo are being compared with (say) crystal structures > for the fitness of those minima as a model of (presumably) what's around > under biological conditions. I'd guess that there's an appreciable number of > cases where this is a three-way absurdity... > > With respect to the MM forcefields optimized for aqua conditions, isn't it more reasonable to minimize the homology models in a waterbox? After all that the native conformation is in aqua solution.
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