Superfold (pred)

[HOME]

[5-tile code prediction by NtileCodePredcitor (superfolds)]

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].

One could use the "NtileCodePredictor" program to estimate "variable" parts (i.e., parts with multiple native structures) and active sites since prediction failure implies that the corresponding amino-acid fragment usually assumes another local structure. (For example, in the case of 1APS shown below, the region of large red spheres coincides with the active site.)

Backbone structures are snapshots by ProteinViewer, where N-terminal is colored red and C-terminal blue.
Backbone structures show the result obtained with option "-f".
Amino acids of failed prediction ("F") are denoted by large red spheres.
Amino acids whose code is contained in the prediction ("c") are denoted by large yellow spheres.
Amino acids without prediction are denoted by small blue spheres.
Click on thumbnail for larger images.
Click ".pred" file to view the predicted 5-tile code sequence.

		option "-f"	option "-5"	option "-7"
Type (PDB id)	Backbone structure (option "-f")	Success rate Ext. suc. rate Coverage	Success rate Ext. suc. rate Coverage	Success rate Ext. suc. rate Coverage
average		0.88 0.91 1.00	0.72 0.87 0.97	0.92 0.92 0.95

Globin-like 1THB		0.91 0.92 1.00 ".pred" file	0.84 0.91 0.98 ".pred" file	0.89 0.92 0.97 ".pred" file
Up-dowm 256B		0.91 0.95 1.00 ".pred" file	0.71 0.89 0.97 ".pred" file	0.96 0.96 0.96 ".pred" file
Alpha-beta-plait 1APS		0.89 0.89 1.00 ".pred" file	0.69 0.87 0.98 ".pred" file	0.96 0.96 0.96 ".pred" file
UB rolls 1UBQ		0.96 0.99 1.00 ".pred" file	0.86 0.93 1.00 ".pred" file	0.96 0.96 0.97 ".pred" file
Doubly wound 2FOX		0.85 0.87 1.00 ".pred" file	0.67 0.82 0.96 ".pred" file	0.89 0.89 0.93 ".pred" file
TIM barrel 7TIM		0.80 0.85 1.00 ".pred" file	0.64 0.80 0.96 ".pred" file	0.87 0.87 0.95 ".pred" file
Trefoil 1I1B		0.82 0.86 1.00 ".pred" file	0.63 0.80 0.92 ".pred" file	0.80 0.80 0.87 ".pred" file
Jelly roll 2BUK		0.88 0.91 1.00 ".pred" file	0.63 0.84 0.99 ".pred" file	0.98 0.98 0.98 ".pred" file
IG-like 2RHE		0.95 0.98 1.00 ".pred" file	0.79 0.92 0.98 ".pred" file	0.96 0.96 0.96 ".pred" file

[References]

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