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353: CASP9 Refinement Puzzle 10

Closed since about 12 years ago



August 10, 2010
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Our last CASP9 Refinement puzzle is the same target from 342: CASP9 Puzzle 34. This is the one of the most challenging refinement targets. There are big deviations from the native structure in the areas around residues 10, 20 and 50. These regions are denoted in note mode (press 3 to enter Note Mode), and your score will not register until you have sufficiently refined this area. Please see the puzzle comments for more info as we will post a different version of this puzzle.

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beta_helix Staff Lv 1

So this last CASP9 refinement target will not be easy.
The CASP9 organizers have told us that the best submitted model for this target had a GDT_TS of 56 which is quite low (a score of 100 is a perfect match to the native).

This means that you will need to heavily refine the starting model, especially in the regions that they mention (residues 10, 20 and 50) shown in note mode.

To make this even harder, the starting model they have selected is the Rosetta model submitted by our human group in the Baker Lab, which is trapped in a local minimum and highly minimized (essentially wiggled to death) so it will be very difficult to improve the score unless you get very close to the native state.

This is why we had to bring back the conditions for this one. It is in your best interest to focus on the regions with conditions immediately from the start (as opposed to wiggling/shaking the starting model) so that your starting very best score will be as low as possible.
This way, hopefully once you've made enough improvements on the 3 regions with conditions you will be able to beat the score of the starting puzzle.

Because we realize how much of a challenge this is, we will also post another version of this puzzle without conditions that will hopefully be useful.