(PS)2-v2: template-based protein structure prediction server

BMC Bioinformatics

Table 3 Comparing S2A2 matrix with other methods for sequence alignment accuracies on the ProSup benchmark

Method	T_c^e	T_m^e	T_i^e	σ₀^e
S2A2^a	8732	947	7198	53.4
S2A2 + PSSM^a	9470	868	6998	58.7
SSALN^b	9256	1115	7245	58.3
SPARKS^c	-	-	-	57.2
prof_sim	8009	4505	3142	43.6
PSI-BLAST	6733	4938	3452	36.4
FASTA^d	5340	3003	7452	31.4

^aThis work.
^bResults from Qiu and Elber [10].
^cResults from Zhou and Zhou [9].
^dResults from Domingues et al. [15].
^eT_c and T_m are total numbers of correctly aligned and missed residue pairs, respectively; T_i is the total number of incorrect aligned pairs; σ₀ is the average percentage of correctly aligned residues

ISSN: 1471-2105