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Table 1: Pairs in the RS126 set that have an SD score of greater than 5. Alignments were generated by the AMPS package[6] a blosum62 matrix, and gap penalty of 10, with 100 randomisations. Fold definitions come from the current release (1.37) of the SCOP database [47]

(1)	(2)	SD score	Fold (1)	Fold(2)
1eca[75]	2lhb[52]	5.12	Globin-like	Globin-like
1azu[76]	2pcy[53]	5.40	Cupredoxins	Cupredoxins
2rspa[77]	5hvpa[56]	5.81	Acid proteases	Acid proteases
1paz[78]	2pcy[53]	7.22	Cupredoxins	Cupredoxins
2lhb[52]	4sdha[79]	7.70	Globin-like	Globin-like
1cdta[80]	3ebx[54]	8.26	Snake toxin-like	Snake toxin-like
3cln[81]	4cpv[55]	8.27	EF Hand-like	EF Hand-like
2gbp[82]	8abp[57]	8.86	Periplasmic binding	Periplasmic binding
1ovoa[83]	1tgsi[51]	9.45	Ovomucoid/PCI-1 like	Ovomucoid/PCI-1 like
1fdlh[84]	1mcpl[50]	12.66	Immunoglobulin	Immunoglobulin
4cms[48]	5er2e [49]	15.98	Acid proteases	Acid proteases

 

 

Table 2: Percentages of secondary structural state per secondary structure definition method

	DSSP[38]	STRIDE[40]	DEFINE[39]
Helix	28.9	29.8	30.2
Sheet	22.9	24.4	30.0
Coil	48.1	45.8	39.7

 

 

Table 3: Ranges of length for secondary structural elements as defined by DSSP[38] STRIDE[40] and DEFINE[39] for the RS126 set

State	Method	Min	Mean	Max	Total number of secondary structures
	DSSP[38]	3	9	54	817
Helix	STRIDE	2	10	51	753
	DEFINE[39]	5	14	65	553
	DSSP	1	4	19	1302
Strand	STRIDE[40]	1	4	19	1303
	DEFINE	4	6	26	1030

 

 

Table 4: Summary statistics of the alignments used in the predictions

	Ave. % ID.	Ave. sequence	Ave. No of sequences
	between sequences	length	per alignment
CB396 set	34	157 residues	18
RS126 set	31	185 residues	30

 

 

Table 5: Data for class types used for the predictions

Class definition	RS126 set No. (%)	CB396 set No. (%)
Alpha and beta (a/b)	25 (20)	107 (27)
Alpha and beta (a+b)	17 (13)	101 (26)
All alpha	27 (21)	68 (17)
All beta	38 (20)	78 (20)
Multi-domain	3 ( 2)	0 ( 0)
Small proteins	18 (14)	27 ( 7)
Membrane	1 ($\le$1)	3 ($\le$1)
Peptides	1 ($\le$1)	12 ( 3)

 

 

Table 6: Q₃ and segment overlap results for the set of RS126, and CB396 proteins

Method	RS126 Protein set		CB396 protein set
	Q3	SOV	Q3	SOV
PHD[64]	73.5	73.5	71.9	75.3
DSC[29]	71.1	71.6	68.4	72.0
PREDATOR[28]	70.3	69.9	68.6	69.8
NNSSP[30]	72.7	70.6	71.4	71.3
CONSENSUS	74.8	74.5	72.9	75.4

 

 

Table 7: Family size for the automatically generated alignments for the RS126 protein set, considering 2 levels of BLAST[59] p-value cutoff

	p-Value cutoff 10-10	p-Value cutoff 10-2
Total Number of Residues	1716356	2013632
Total Number of Sequences	7013	8974
Average Number of Sequences per Family	55.6	71.2

 

 

Table 8: Comparison of the of Q₃ accuracy for a decrease in the BLAST[59] P-value cut-off from 10^-10 to 10^-2 with the RS126 set. (The alignments used for these predictions did not use a percentage identity filter)

	p-value cutoff	10-10	p-value cutoff	10-2
Method	DSSP	STRIDE	DSSP	STRIDE
PHD[64]	72.4	72.4	73.2	73.2
DSC[29]	70.2	70.0	71.0	70.7
PREDATOR[58]	69.7	69.3	70.7	70.3
NNSSP [30]	71.8	71.2	72.4	71.7
MULPRED	66.7	65.4	67.2	66.8
ZPRED [26]	65.5	64.7	66.7	65.9
CONSENSUS	73.9	73.7	74.5	74.3

 

 

Table 9: Effect on Q₃ accuracy by removing all sequences similar to the query at different % identity thresholds, using the RS126 protein set

	100%	95%	80%	75%	60%
PHD[64]	73.2	73.3	73.4	73.5	73.3
DSC[29]	71.0	71.0	71.0	71.1	70.9
PREDATOR[28]	70.7	70.4	70.1	70.3	70.4
NNSSP[30]	72.4	72.5	72.7	72.7	72.8
CONSENSUS	74.5	74.5	74.6	74.8	74.7
Total No. of Sequences	8974	5907	4320	3833	2681
Ave No. of Sequences/Alignment	71	47	34	30	20

 

 

Table 10: Mean percentages of secondary structure state defined by DSSP[38] when different 8 to 3 state reduction methods are used

	Mean % of Helix	Mean % of Sheet	Mean % of Coil
Method A	28.9	22.9	48.1
Method B	25.3	21.2	52.6
Method C	25.6	21.2	52.3

 

 

Table 11: Changing 8 to 3 state reduction, for DSSP and resultant Q₃ accuracy for the consensus method, based on the RS126 set of proteins

Change	Q3
Reduction method A[64]	74.8
B $\rightarrow$ Coil only	75.7
G $\rightarrow$ Coil only	76.6
B and G $\rightarrow$ Coil	77.5
GGGHHHH $\rightarrow$ HHHHHHH, B and G $\rightarrow$ Coil (Method C)[30]	77.5
B, G and HHHH EE $\rightarrow$ Coil (Method B)[58]	77.9

 

 

Table 12: Results for the RS126 protein set, by reducing the definition to 3 state by methods A and B

Method	DSSP (A)	STRIDE (A)	DSSP (B)	STRIDE (B)
PHD[64]	73.5	73.5	76.3	76.3
DSC[29]	71.1	70.9	73.3	73.4
PREDATOR[28]	70.3	69.6	75.2	74.0
NNSSP[30]	72.7	72.2	77.3	76.5
CONSENSUS	74.8	74.7	77.9	77.9

 

 

Table 13: Results for single sequence prediction methods via a full jack-knife test. The column 'Author' is the authors jack-knife value for the method with their dataset, and definition reduction method. All results are calculated using reduction method A, and also converting G and B states to coil. For PHD[64] the authors quote 71.6% as their cross-validated accuracy. However, G and B states were considered in the accuracy calculation for PHD[64]

Method	RS126	CB396	Author
PHD[64]	76.3	74.2	-
SIMPA[72]	67.3	67.6	67.7
GOR IV[74]	53.3	64.6	64.4
SOPM[73]	66.8	64.7	69.0

 

  

Figure 1: Comparison of segment length distributions for each definition method