Closed since almost 12 years ago
Advanced Overall Prediction CASP11The first CASP11 refinement target is larger than most Foldit puzzles, at 201 residues. This model was the best server prediction for target T0760, generated by the MULTICOM-NOVEL server. We've been told that ~58% of this model matches the native! As this is such a large protein, we are giving you 10 days to work on it. More info in the puzzle comments, where you can post your feedback about whether puzzles of this size are too much for us to tackle in CASP11.
This is the page for this CASP11 refinement target:
http://predictioncenter.org/casp11/target.cgi?id=32
Note that the organizers gave us this hint:
"Starting model's GDT_HA=58"
GDT_TS=58 essentially means that 58% of the model superimposes correctly onto the native structure: http://en.wikipedia.org/wiki/Global_distance_test
So please give us your feedback about whether or not 10 days is sufficient for such a large puzzle, or if you feel we shouldn't participate at all in these larger CASP11 refinement puzzles.
For example, the second refinement target, TR762, has 257 residues… so we will NOT be posting that one!
Thank you for your input…
58 percent would most likey be similar to tracing a line and staying on the line 58 percent of the time? not so much that large sections are spot on, and the there is a forty two percent section that needs to be worked on? i only ask because segment 75 is looking like a nice place for a cutpoint and then adjusting both halves of the protein to mesh better with each other.
after wiggling it out, i see that it wouldn't be wise not to make major renovations. refinement of the typical kind is most likely.
Five days/ten days…that isn't the issue. This size is simply too large to run with other puzzles. Since you asked, my vote is no to this size.
Here is the sequence logo predicted by the SAM server:
H = helix
E = sheet
C = loop (or coil)
The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.
Note that these secondary structure predictions are not necessarily present in the starting structure that has been provided in the puzzle.
If you are a new Foldit player, please make sure you have completed all these tutorials before trying this puzzle:
Thanks bkoep for the secondary structure reduction.
May I suggest you to provide also the sequence in writing, so that we can immediately copy it into our puzzle using available scripts?
Could you not create a tool that allows cut sections of the protein to be saved as new tracks ? ie
Cut at residue 7
Cut at residue 54
Right click context menu
Save cut section as…track 1
??
Click on the CASP link on the first comment:
http://fold.it/portal/node/997715#comment-27759
and it will point you to this page with the sequence:
http://predictioncenter.org/casp11/target.cgi?target=TR760&view=sequence
Puzzles of this size were pretty well unplayable in Legacy. NC only makes the situation substantially worse. Even puzzle 894 at 163 segs is now 'pushing it'. Playable only to a moderate level of investigation by many - and this at the cost of running just one client and ignoring other puzzles.
