Table 2.

The contribution of individual terms to the alignment accuracy for Prosup and SALIGN benchmarks

	Prosup (%)		SALIGN		Prosup (%)		SALIGN
Method	1–1a	≤4b	1–1c (%)	Method	1–1a	≤4b	1–1c (%)
PSSMd	63.4	80.5	59.1	SP−Xe	72.7	90.1	65.9
+SSf	68.4	87.1	62.9	−SSg	72.4	88.7	64.7
+ϕ/ψf	68.7	85.5	61.7	−ϕ/ψg	72.3	90.2	65.5
+ASAf	70.2	86.7	63.9	−ASAg	69.3	86.3	62.1

^aOne-to-one match given by the method and Prosup.

^bWithin four residues by the method and Prosup.

^cOne-to-one match given by the method and TMalign.

^dUsing PSSM matrix from PSIBLAST only.

^eSP-X: SPARKS-X.

^fUsing PSSM plus secondary structure, or ϕ/ψ, or ASA as noted.

^gExcluding secondary structure, or ϕ/ψ, or ASA as noted.