4 ms·

I'm biased since I do simulations but you're being too harsh on force fields. All the proteins in the paper I mentioned had their structure correctly predicted

• timr 13y ago
  "That's a serious accomplishment compared to the decade-old papers you're citing." What? It's not like the "decade-old" paper has become less correct over time. I mean, it's great that MD is finally close to predicting something that could be predicted a decade ago with much simpler methods, but that isn't saying a lot. Plus, as the other commenter pointed out, there's a complicated cross-validation problem that biases the results you're reporting. In truly blind tests (i.e. CASP), MD force fields just aren't that good at predicting structure from sequence. The usual counter-argument is that they aren't meant to work with non-MD methods (fair enough, I guess), but you don't have to try very hard to find reasons not to trust them. MD simulations have always been very finicky things, requiring lots of manual intervention to get "right".