Table 2.

Average accuracy on long-range contacts for the element alignment predictor

	E–E			H–H			E–E			H–H
Class	L/5	L/10	Best 5	L/5	L/10	Best 5	L/5	L/10	Best 5	L/5	L/10	Best 5
All	0.24	0.25	0.25	0.09	0.10	0.10	0.35	0.36	0.37	0.11	0.12	0.13
All-alpha	—	—	—	0.09	0.10	0.11	—	—	—	0.10	0.11	0.11
All-beta	0.19	0.21	0.20	—	—	—	0.19	0.17	0.17	—	—	—
Alpha/beta	0.22	0.19	0.21	0.07	0.07	0.07	0.52	0.55	0.54	0.11	0.14	0.12
Alpha + beta	0.26	0.27	0.27	0.08	0.08	0.08	0.34	0.37	0.35	0.09	0.11	0.10

Contact prediction accuracy (Acc, see Section 2.1) of the element alignment predictor for long-range residue pairs. The length L refers to the sum of the lengths of helix/strand elements in the protein sequence. The protein domains having <5 contacts in the strand–strand and helix–helix regions have been excluded from the evaluation. The strand–strand predictions on the All-alpha class, as well as the helix-helix predictions on the All-beta class, are not included. The performance on the strand–strand regions, E–E, E–E and helix–helix regions, H–H, H–H, are obtained by using the contact probabilities in Equations (10), (12), (11) and (13), respectively.