super7old (dsgn)

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[Amino acid prediction by NtileCodePredcitor (superfolds)]

Here "protein design" means prediction of the amino acid sequence of a given 5-tile code sequence.

Superfolds are the protein folds known to recur in proteins having neither sequence nor functional similarity.
And they are much common than other folds. See also [1].

Backbone structures are snapshots by ProteinViewer, where N-terminal is colored red and C-terminal blue.
Backbone structures show the result obtained with the "-2" option.
5-tile codes of successful prediction ("_") are denoted by large blue spheres.
5-tile codes whose corresponding amino acid is contained in the prediction ("c") are denoted by large yellow spheres.
5-tile codes with no hit ("-") , i.e., "new structure", are denoted by small red spheres.
5-tile codes with hit count less than five, i.e., "rare structure", are denoted by small orange spheres.
5-tile codes with hit count more than 999, i.e., "popular structure", are denoted by small blue spheres.
Click on thumbnail for larger images.
Click "_dsgn.pred" file to view the predicted 5-tile code sequence.

		option "-7"	option "-9"	option "-1"	option "-2"	option "-3"
Type (PDB id)	Backbone structure (opton "-2")	Success rate Ext. suc. rate Coverage	Success rate Ext. suc. rate Coverage	Success rate Ext. suc. rate Coverage	Success rate Ext. suc. rate Coverage	Success rate Ext. suc. rate Coverage
average		0.16 0.17 1.00	0.20 0.21 1.00	0.36 0.38 0.99	0.58 0.63 0.95	0.55 0.57 0.70

Globin-like 1THB		0.21 0.22 1.00 "_dsgn.pred" file	0.26 0.28 1.00 "_dsgn.pred" file	0.31 0.33 0.96 "_dsgn.pred" file	0.61 0.64 0.95 "_dsgn.pred" file	0.46 0.51 0.70 "_dsgn.pred" file
Up-dowm 256B		0.19 0.19 1.00 "_dsgn.pred" file	0.21 0.21 1.00 "_dsgn.pred" file	0.23 0.24 1.00 "_dsgn.pred" file	0.34 0.36 0.99 "_dsgn.pred" file	0.51 0.54 0.99 "_dsgn.pred" file
Alpha-beta-plait 1APS		0.16 0.16 1.00 "_dsgn.pred" file	0.14 0.17 1.00 "_dsgn.pred" file	0.44 0.47 1.00 "_dsgn.pred" file	0.91 0.92 0.98 "_dsgn.pred" file	0.96 0.96 0.96 "_dsgn.pred" file
UB rolls 1UBQ		0.18 0.18 1.00 "_dsgn.pred" file	0.22 0.22 1.00 "_dsgn.pred" file	0.50 0.50 1.00 "_dsgn.pred" file	0.72 0.78 1.00 "_dsgn.pred" file	0.58 0.62 0.97 "_dsgn.pred" file
Doubly wound 2FOX		0.14 0.14 1.00 "_dsgn.pred" file	0.13 0.14 1.00 "_dsgn.pred" file	0.28 0.29 1.00 "_dsgn.pred" file	0.37 0.43 0.93 "_dsgn.pred" file	0.00 0.00 0.00 "_dsgn.pred" file
TIM barrel 7TIM		0.18 0.18 1.00 "_dsgn.pred" file	0.19 0.21 1.00 "_dsgn.pred" file	0.38 0.43 0.93 "_dsgn.pred" file	0.45 0.49 0.82 "_dsgn.pred" file	0.37 0.41 0.53 "_dsgn.pred" file
Trefoil 1I1B		0.13 0.13 1.00 "_dsgn.pred" file	0.14 0.14 1.00 "_dsgn.pred" file	0.14 0.17 0.99 "_dsgn.pred" file	0.23 0.39 0.87 "_dsgn.pred" file	0.19 0.21 0.21 "_dsgn.pred" file
Jelly roll 2BUK		0.11 0.12 1.00 "_dsgn.pred" file	0.20 0.20 1.00 "_dsgn.pred" file	0.45 0.49 1.00 "_dsgn.pred" file	0.80 0.85 1.00 "_dsgn.pred" file	0.98 0.98 0.98 "_dsgn.pred" file
IG-like 2RHE		0.17 0.17 1.00 "_dsgn.pred" file	0.29 0.29 1.00 "_dsgn.pred" file	0.52 0.54 1.00 "_dsgn.pred" file	0.79 0.80 1.00 "_dsgn.pred" file	0.87 0.87 0.96 "_dsgn.pred" file

[References]

C.A. Orengo, D.T. Jones, and J.M. Thornton, Protein super7amilies and domain superfolds. Nature 372, 631-634 (1994).