While it's nice to hear that you're finally starting to incorporate cut-points into Foldit, I have several clarification questions:
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So exactly what's going on with the protein involved in 482/485? Given the lack of a crystal structure, is the NMR model considered an accurate "native"? (Again, I'm asking because I was surprised that my team's top solution scored much better than Model 1.)
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In addition to cut-points, also important would be the ability to align the template like a guide when doing partial threading– in other words, be able to copy the backbone configuration relative to the local selected region rather than the whole protein. This would make it MUCH easier to mix-and-match solutions when two templates differ significantly.
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For the sake of fairness, would you recommend that I forfeit my first-place finish due to the use of 2L3B? And for future purposes, would you prefer that I make the information public if there is a good template from a public database available for a specific puzzle (as long as the sequence isn't an exact match)?
To answer your first question, this NMR model is considered as accurate a native as anything solved so far for this protein, but if you look at the variation across all 20 NMR models:
you can see that there is no 1 correct native solution. So, while your Foldit prediction was different from Model 1 of 2l3b, it was actually closer to some of the other models in the NMR ensemble (http://www.pdb.org/pdb/explore/explore.do?structureId=2L3B)
As the MPMV-PR case showed quite clearly, sometimes NMR models aren't "correct", but when that is the only model available (until Foldit players solve the crystal structure ;-) it's considered to be the native.
To answer your third question, there will be no forfeiting of points from anyone.
If you want my honest opinion for what I would prefer for future purposes… ideally (other than CASP or structures where we ask you to help solve the unknown structure) nobody would try to look up any templates, homologs or natives.
Because if we are posting a puzzle to test out new tools then we want you to try to fold using the new tools (not looking up extra external information). Now, we realize that is a tough request to ask so we have never explicitly ask any players not to do that, but we noticed this issue back when we started writing the first Nature paper.
There was no way that we could publish any non-blind results when it was clear that players were able to look up natives.
Again, if we want to discuss this further, I will be happy to continue in a different feedback/forum. This feedback is asking a different question, which I believe I answered previously, so I am closing this thread.
