<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div class="h5"><br></div></div> 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...<br>
<br></blockquote><div><br>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. <br>
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