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579: Beginner CASP10 Refinement Puzzle: TR662
Status: Closed
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Soloists
| 1 | enszyme 123 98 | L'Alliance Francophone | 9,917 | 100 | | 2 | smilingone 9 19 | Go Science | 9,917 | 98 | | 3 | BitSpawn 135 631 | Anthropic Dreams | 9,914 | 95 | | 4 | spmm 135 2177 | Void Crushers | 9,912 | 92 | | 5 | meatexplosion 89 25 | Anthropic Dreams | 9,909 | 90 | | 6 | Bletchley Park 10 6 | Contenders | 9,896 | 87 | | 7 | mimi 12 21 | Contenders | 9,895 | 85 | | 8 | jtollenaar 135 439 | | 9,894 | 83 | | 9 | O Seki To 44 14 | Team Hungary | 9,894 | 80 | | 10 | utaca 76 33 | | 9,891 | 78 | | 11 | dembones 69 121 | Contenders | 9,890 | 76 | | 12 | randomlil 135 6358 | Go Science | 9,889 | 74 | | 13 | hansvandenhof 16 9 | foldeRNA | 9,885 | 71 | | 14 | Madde 106 31 | Void Crushers | 9,884 | 69 | | 15 | saint Jean 96 52 | L'Alliance Francophone | 9,883 | 67 | | 16 | christioanchauvin 47 38 | L'Alliance Francophone | 9,883 | 65 | | 17 | pauldunn 28 22 | Go Science | 9,882 | 64 | | 18 | pgiles 135 57 | | 9,882 | 62 | | 19 | bertro 32 10 | foldeRNA | 9,880 | 60 | | 20 | jakbinimbol 135 7 | | 9,879 | 58 | | 21 | grogar7 56 41 | | 9,875 | 56 | | 22 | gramps 70 27 | Anthropic Dreams | 9,874 | 55 | | 23 | Rav3n_pl 135 178 | Anthropic Dreams | 9,872 | 53 | | 24 | Acida-2 135 1084 | | 9,869 | 52 | | 25 | nemo7731 135 54 | | 9,868 | 50 |
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This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=110&view=refinement
Note that the organizers give us this as a hint:
"N-term res. 1-4 are disordered in the native structure and removed from the starting model. Starting GDT_TS=84."
So, the first 4 residues have been deleted.
GDT_TS=84 essentially means that 84% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test
We believe that Zhang-Server_TS4.pdb is identical to the refinement model (except that it obviously doesn't have the first 4 residues trimmed!)
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.
For example, the Valines at residues 8, 11, 35-36, 62 & 69 are highly predicted to be part of a helix. However, the Valines at residues 49 & 52 are predicted to be in either loops or sheets.