Reply To: how to get reliable results for carbohydrate docking?

[Anonymous]

Rosetta’s score function is probably too greedy (or perhaps just insufficiently aware of entropy) for it to dock only part of a sugar the way you are suggesting.

You can try playing with scorefunction weights – if you weaken the long-range hydrogen bond terms, then perhaps Rosetta will make only the strongest (most real) hydrogen bonds to your carbohydrate.

You could also do the experiment I described iteratively. Try it with each different part of the molecule as “real” and the others virtualized, and see which set of models has the best scores – that’s Rosetta’s prediction.