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EVA summary for category sec (3)

Contents

Local link to information about methods evaluated
All prediction results for secondary structure
All prediction results in ASCII (raw text)
Explanations of measures for prediction accuracy
For older versions of the results

About secondary structure prediction methods evaluated

Method	Nprot	Nweek	Detailed results for method
ALL	306	58	method/index.html

APSSP	26	9	method/apssp.html
JPred	235	50	method/jpred.html
PHD	287	57	method/phd.html
PHDpsi	287	57	method/phdpsi.html
PROF0	195	38	method/prof0.html
PROF	282	55	method/prof1.html
PROF_king	221	43	method/prof_king.html
PSIpred	281	56	method/psipred.html
PSSP	254	47	method/pssp.html
SAM-T99sec	173	41	method/samt99_sec.html
SSpro	245	44	method/sspro.html

Comparison of secondary structure prediction methods (detail level 3)

Averages compiled over different subsets

The reason for compiling different averages is that not ALL proteins were predicted by all methods!
Only proteins with no significant sequence identity to previously known PDB proteins are reported, here.
The following subsets are given:
- set 1: 14 proteins and 8 methods (HTML - ASCII)
- set 2: 115 proteins and 8 methods (HTML - ASCII)
- set 3: 118 proteins and 7 methods (HTML - ASCII)
- set 4: 203 proteins and 6 methods (HTML - ASCII)
- set 5: 279 proteins and 4 methods (HTML - ASCII)
Detail level 3 (this file) as ASCII

subset	nprot	sots	rank	method	Q3	ERRsigQ3	Q3H%o	ERRsigQ3H%o	Q3H%p	ERRsigQ3H%p	Q3E%o	ERRsigQ3E%o	Q3E%p	ERRsigQ3E%p	Q3L%o	ERRsigQ3L%o	Q3L%p	ERRsigQ3L%p	sov	ERRsigsov	sovH	ERRsigsovH	sovE	ERRsigsovE	sovL	ERRsigsovL	BAD	ERRsigBAD	info	ERRsiginfo	corrH	ERRsigcorrH	corrE	ERRsigcorrE	corrL	ERRsigcorrL	class	ERRsigclass	contDH	ERRsigcontDH	contDE	ERRsigcontDE
Set 1			Sorted alphabetically for identical ranks!		MORE SCORES
common 1	14	dssp	1	JPred	70.5	+/-3.8	72.3	+/-12.9	84.0	+/-14.1	57.6	+/-9.8	73.5	+/-12.3	79.7	+/-2.8	70.1	+/-5.4	67.9	+/-5.9	54.1	+/-10.3	62.1	+/-8.6	68.4	+/-5.7	2.7	+/-1.3	0.27	+/-0.04	0.66	+/-0.10	0.58	+/-0.09	0.54	+/-0.06	71.4	+/-12.5	10.1	+/-1.9	8.9	+/-3.2
				PHD	71.3	+/-2.9	75.8	+/-11.1	76.9	+/-9.8	60.3	+/-9.9	61.8	+/-10.6	76.1	+/-3.8	72.6	+/-4.6	63.7	+/-3.3	61.4	+/-8.5	60.9	+/-7.9	64.6	+/-2.6	4.5	+/-1.3	0.27	+/-0.03	0.61	+/-0.08	0.52	+/-0.08	0.49	+/-0.04	78.6	+/-11.4	7.5	+/-1.8	9.9	+/-1.9
				PHDpsi	70.3	+/-2.7	77.7	+/-12.7	80.6	+/-11.8	63.1	+/-9.6	67.4	+/-10.9	74.1	+/-2.7	72.1	+/-4.6	62.1	+/-3.4	53.9	+/-8.9	65.9	+/-6.9	59.0	+/-3.4	4.1	+/-1.3	0.26	+/-0.03	0.66	+/-0.11	0.57	+/-0.08	0.53	+/-0.04	85.7	+/-9.7	7.3	+/-1.6	7.5	+/-1.9
				PROF	72.3	+/-3.3	79.6	+/-13.1	82.9	+/-13.2	68.8	+/-10.8	70.1	+/-11.7	73.9	+/-2.6	74.9	+/-4.4	69.4	+/-4.5	56.4	+/-10.1	71.1	+/-7.1	66.5	+/-4.5	3.9	+/-1.8	0.30	+/-0.03	0.69	+/-0.11	0.62	+/-0.08	0.56	+/-0.04	92.9	+/-7.1	7.6	+/-1.9	7.2	+/-2.2
				PSIpred	72.7	+/-2.3	82.1	+/-10.2	82.0	+/-10.3	68.9	+/-12.4	72.1	+/-12.4	70.8	+/-3.2	75.2	+/-4.5	67.4	+/-4.9	72.2	+/-8.6	65.0	+/-9.3	62.1	+/-4.5	0.8	+/-0.3	0.30	+/-0.04	0.70	+/-0.08	0.64	+/-0.10	0.57	+/-0.07	85.7	+/-9.7	8.4	+/-2.5	4.6	+/-1.9
				SAM-T99sec	71.8	+/-2.8	83.6	+/-10.1	77.9	+/-9.3	63.1	+/-10.3	75.3	+/-12.5	70.6	+/-3.9	75.3	+/-4.7	65.0	+/-4.3	68.4	+/-7.6	64.6	+/-8.3	61.8	+/-4.5	2.2	+/-0.7	0.29	+/-0.04	0.68	+/-0.08	0.62	+/-0.09	0.54	+/-0.06	92.9	+/-7.1	8.7	+/-2.2	5.7	+/-2.5
common 1	14	dssp	2	APSSP	62.9	+/-3.0	63.5	+/-10.9	67.9	+/-10.6	32.5	+/-6.5	48.9	+/-9.8	76.4	+/-3.5	64.3	+/-4.9	49.4	+/-4.1	44.6	+/-8.9	42.4	+/-9.7	55.4	+/-3.8	5.8	+/-1.4	0.14	+/-0.03	0.45	+/-0.09	0.28	+/-0.10	0.37	+/-0.05	78.6	+/-11.4	7.6	+/-1.9	15.4	+/-3.0
				PSSP	64.0	+/-2.8	63.0	+/-9.5	71.2	+/-9.7	54.7	+/-9.5	47.6	+/-9.5	68.1	+/-3.2	67.1	+/-5.4	53.4	+/-3.3	57.7	+/-8.9	55.9	+/-8.6	53.4	+/-3.2	5.0	+/-1.3	0.19	+/-0.03	0.48	+/-0.08	0.38	+/-0.10	0.37	+/-0.06	64.3	+/-13.3	8.2	+/-1.5	11.4	+/-2.3

subset	nprot	sots	rank	method	Q3	ERRsigQ3	Q3H%o	ERRsigQ3H%o	Q3H%p	ERRsigQ3H%p	Q3E%o	ERRsigQ3E%o	Q3E%p	ERRsigQ3E%p	Q3L%o	ERRsigQ3L%o	Q3L%p	ERRsigQ3L%p	sov	ERRsigsov	sovH	ERRsigsovH	sovE	ERRsigsovE	sovL	ERRsigsovL	BAD	ERRsigBAD	info	ERRsiginfo	corrH	ERRsigcorrH	corrE	ERRsigcorrE	corrL	ERRsigcorrL	class	ERRsigclass	contDH	ERRsigcontDH	contDE	ERRsigcontDE
Set 2			Sorted alphabetically for identical ranks!		MORE SCORES
common 2	115	dssp	1	JPred	75.5	+/-0.9	72.3	+/-2.8	84.0	+/-3.1	57.6	+/-3.1	73.5	+/-3.8	80.6	+/-1.4	69.1	+/-1.2	68.9	+/-1.5	69.6	+/-2.5	65.7	+/-2.8	66.9	+/-1.6	1.7	+/-0.2	0.34	+/-0.02	0.66	+/-0.02	0.58	+/-0.03	0.54	+/-0.02	78.3	+/-3.9	6.9	+/-0.7	5.4	+/-0.5
				PHDpsi	74.6	+/-0.9	77.7	+/-2.7	80.6	+/-2.8	63.1	+/-3.3	67.4	+/-3.5	71.1	+/-1.4	72.9	+/-1.2	68.8	+/-1.3	71.9	+/-2.3	67.7	+/-2.7	64.0	+/-1.6	2.7	+/-0.3	0.24	+/-0.07	0.66	+/-0.02	0.57	+/-0.03	0.53	+/-0.02	80.0	+/-3.7	6.7	+/-0.7	4.7	+/-0.5
				PROF	76.4	+/-0.9	79.6	+/-2.6	82.9	+/-2.7	68.8	+/-3.5	70.1	+/-3.5	72.6	+/-1.5	74.8	+/-1.2	71.8	+/-1.4	73.8	+/-2.2	71.3	+/-2.7	67.6	+/-1.6	2.2	+/-0.2	0.34	+/-0.01	0.69	+/-0.02	0.62	+/-0.02	0.56	+/-0.02	82.6	+/-3.5	6.1	+/-0.7	4.0	+/-0.4
				PSIpred	76.5	+/-1.0	82.1	+/-2.6	82.0	+/-2.8	68.9	+/-3.6	72.1	+/-3.7	74.6	+/-1.3	74.5	+/-1.2	71.7	+/-1.5	76.9	+/-2.2	69.0	+/-2.8	68.2	+/-1.5	2.2	+/-0.3	0.36	+/-0.02	0.70	+/-0.02	0.64	+/-0.03	0.57	+/-0.02	83.5	+/-3.5	5.9	+/-0.7	4.3	+/-0.5
				SAM-T99sec	76.3	+/-0.9	83.6	+/-2.7	77.9	+/-2.6	63.1	+/-3.2	75.3	+/-3.8	70.5	+/-1.8	74.7	+/-1.5	70.9	+/-1.4	75.0	+/-2.2	69.1	+/-2.6	65.0	+/-1.8	1.6	+/-0.2	0.35	+/-0.01	0.68	+/-0.02	0.62	+/-0.02	0.54	+/-0.02	81.7	+/-3.6	6.5	+/-0.8	4.4	+/-0.5
				SSpro	76.1	+/-1.0	81.4	+/-2.6	82.2	+/-2.7	63.6	+/-3.4	72.4	+/-3.8	75.2	+/-1.3	74.3	+/-1.2	69.2	+/-1.6	75.0	+/-2.2	67.4	+/-2.8	66.0	+/-1.7	2.2	+/-0.3	0.35	+/-0.02	0.70	+/-0.02	0.61	+/-0.02	0.57	+/-0.02	80.0	+/-3.7	6.6	+/-0.8	5.4	+/-0.6
common 2	115	dssp	2	PHD	72.1	+/-1.0	75.8	+/-2.7	76.9	+/-2.8	60.3	+/-3.1	61.8	+/-3.2	67.9	+/-1.4	71.7	+/-1.3	67.4	+/-1.4	70.5	+/-2.3	66.8	+/-2.7	62.4	+/-1.5	3.5	+/-0.3	0.21	+/-0.07	0.61	+/-0.02	0.52	+/-0.03	0.49	+/-0.02	80.0	+/-3.7	7.9	+/-0.8	5.4	+/-0.5
common 2	115	dssp	3	PSSP	63.6	+/-1.0	63.0	+/-2.5	71.2	+/-2.8	54.7	+/-2.8	47.6	+/-2.7	64.9	+/-1.3	64.4	+/-1.3	57.8	+/-1.2	58.0	+/-2.2	62.0	+/-2.6	56.7	+/-1.5	6.5	+/-0.5	0.19	+/-0.01	0.48	+/-0.02	0.38	+/-0.03	0.37	+/-0.02	72.2	+/-4.2	9.7	+/-0.9	8.1	+/-0.7

subset	nprot	sots	rank	method	Q3	ERRsigQ3	Q3H%o	ERRsigQ3H%o	Q3H%p	ERRsigQ3H%p	Q3E%o	ERRsigQ3E%o	Q3E%p	ERRsigQ3E%p	Q3L%o	ERRsigQ3L%o	Q3L%p	ERRsigQ3L%p	sov	ERRsigsov	sovH	ERRsigsovH	sovE	ERRsigsovE	sovL	ERRsigsovL	BAD	ERRsigBAD	info	ERRsiginfo	corrH	ERRsigcorrH	corrE	ERRsigcorrE	corrL	ERRsigcorrL	class	ERRsigclass	contDH	ERRsigcontDH	contDE	ERRsigcontDE
Set 3			Sorted alphabetically for identical ranks!		MORE SCORES
common 3	118	dssp	1	JPred	75.4	+/-0.9	72.3	+/-2.8	84.0	+/-3.0	57.6	+/-3.0	73.5	+/-3.7	80.7	+/-1.3	69.1	+/-1.2	69.0	+/-1.4	69.0	+/-2.5	66.1	+/-2.7	67.2	+/-1.5	1.7	+/-0.2	0.34	+/-0.01	0.66	+/-0.02	0.58	+/-0.03	0.54	+/-0.02	78.8	+/-3.8	7.0	+/-0.7	5.4	+/-0.5
				PHDpsi	74.6	+/-0.9	77.7	+/-2.7	80.6	+/-2.8	63.1	+/-3.2	67.4	+/-3.4	71.2	+/-1.4	73.0	+/-1.2	69.0	+/-1.3	72.0	+/-2.2	68.0	+/-2.7	64.3	+/-1.6	2.7	+/-0.3	0.25	+/-0.07	0.66	+/-0.02	0.57	+/-0.02	0.53	+/-0.02	80.5	+/-3.7	6.6	+/-0.7	4.7	+/-0.5
				PROF	76.3	+/-0.9	79.6	+/-2.5	82.9	+/-2.6	68.8	+/-3.4	70.1	+/-3.4	72.7	+/-1.4	74.7	+/-1.2	71.8	+/-1.3	73.4	+/-2.1	71.4	+/-2.6	67.7	+/-1.5	2.1	+/-0.2	0.34	+/-0.01	0.69	+/-0.02	0.62	+/-0.02	0.56	+/-0.02	83.1	+/-3.5	6.1	+/-0.7	3.9	+/-0.4
				PSIpred	76.4	+/-0.9	82.1	+/-2.6	82.0	+/-2.7	68.9	+/-3.5	72.1	+/-3.7	74.5	+/-1.2	74.4	+/-1.2	71.8	+/-1.4	76.4	+/-2.2	69.4	+/-2.7	68.3	+/-1.5	2.2	+/-0.3	0.36	+/-0.02	0.70	+/-0.02	0.64	+/-0.03	0.57	+/-0.02	83.9	+/-3.4	5.8	+/-0.6	4.3	+/-0.5
				SAM-T99sec	76.2	+/-0.9	83.6	+/-2.7	77.9	+/-2.6	63.1	+/-3.2	75.3	+/-3.7	70.8	+/-1.7	74.6	+/-1.5	70.9	+/-1.3	74.6	+/-2.2	69.3	+/-2.5	65.2	+/-1.7	1.7	+/-0.2	0.35	+/-0.01	0.68	+/-0.02	0.62	+/-0.02	0.54	+/-0.02	82.2	+/-3.5	6.5	+/-0.8	4.3	+/-0.5
				SSpro	76.1	+/-1.0	81.4	+/-2.6	82.2	+/-2.6	63.6	+/-3.3	72.4	+/-3.7	75.4	+/-1.3	74.3	+/-1.1	69.3	+/-1.6	74.6	+/-2.2	67.7	+/-2.7	66.3	+/-1.6	2.2	+/-0.3	0.35	+/-0.02	0.70	+/-0.02	0.61	+/-0.02	0.57	+/-0.02	80.5	+/-3.7	6.6	+/-0.7	5.3	+/-0.5
common 3	118	dssp	2	PHD	72.1	+/-0.9	75.8	+/-2.6	76.9	+/-2.7	60.3	+/-3.0	61.8	+/-3.1	68.1	+/-1.4	71.8	+/-1.2	67.6	+/-1.3	70.5	+/-2.2	67.1	+/-2.6	62.7	+/-1.5	3.5	+/-0.3	0.21	+/-0.07	0.61	+/-0.02	0.52	+/-0.03	0.49	+/-0.01	80.5	+/-3.7	7.8	+/-0.8	5.4	+/-0.5

subset	nprot	sots	rank	method	Q3	ERRsigQ3	Q3H%o	ERRsigQ3H%o	Q3H%p	ERRsigQ3H%p	Q3E%o	ERRsigQ3E%o	Q3E%p	ERRsigQ3E%p	Q3L%o	ERRsigQ3L%o	Q3L%p	ERRsigQ3L%p	sov	ERRsigsov	sovH	ERRsigsovH	sovE	ERRsigsovE	sovL	ERRsigsovL	BAD	ERRsigBAD	info	ERRsiginfo	corrH	ERRsigcorrH	corrE	ERRsigcorrE	corrL	ERRsigcorrL	class	ERRsigclass	contDH	ERRsigcontDH	contDE	ERRsigcontDE
Set 4			Sorted alphabetically for identical ranks!		MORE SCORES
common 4	203	dssp	1	PROF	76.3	+/-0.6	79.6	+/-2.0	82.9	+/-2.0	68.8	+/-2.6	70.1	+/-2.6	74.3	+/-1.0	74.2	+/-0.8	72.1	+/-1.0	73.3	+/-1.6	71.5	+/-1.9	68.5	+/-1.1	2.3	+/-0.2	0.35	+/-0.01	0.69	+/-0.01	0.62	+/-0.02	0.56	+/-0.01	81.3	+/-2.7	6.1	+/-0.5	4.0	+/-0.3
				PSIpred	76.2	+/-0.7	82.1	+/-1.9	82.0	+/-2.0	68.9	+/-2.6	72.1	+/-2.7	75.3	+/-0.9	73.9	+/-0.9	71.5	+/-1.1	76.1	+/-1.6	69.9	+/-2.0	68.3	+/-1.1	2.3	+/-0.2	0.36	+/-0.01	0.70	+/-0.02	0.64	+/-0.02	0.57	+/-0.01	80.8	+/-2.8	5.8	+/-0.5	4.6	+/-0.4
				SSpro	75.9	+/-0.7	81.4	+/-2.0	82.2	+/-2.0	63.6	+/-2.4	72.4	+/-2.7	75.8	+/-0.9	73.8	+/-0.9	70.3	+/-1.1	74.0	+/-1.6	68.9	+/-1.9	67.2	+/-1.2	2.4	+/-0.2	0.35	+/-0.01	0.70	+/-0.02	0.61	+/-0.02	0.57	+/-0.01	81.8	+/-2.7	6.1	+/-0.5	5.1	+/-0.4
common 4	203	dssp	2	JPred	74.6	+/-0.7	72.3	+/-2.1	84.0	+/-2.3	57.6	+/-2.3	73.5	+/-2.8	82.1	+/-0.9	68.3	+/-0.9	69.1	+/-1.1	68.9	+/-1.9	66.3	+/-2.0	68.2	+/-1.1	2.3	+/-0.2	0.33	+/-0.01	0.66	+/-0.02	0.58	+/-0.02	0.54	+/-0.01	76.8	+/-3.0	7.8	+/-0.5	5.7	+/-0.4
				PHDpsi	74.4	+/-0.6	77.7	+/-2.0	80.6	+/-2.1	63.1	+/-2.4	67.4	+/-2.5	72.5	+/-1.0	72.5	+/-0.8	69.0	+/-1.0	71.7	+/-1.7	68.0	+/-1.9	64.9	+/-1.2	2.9	+/-0.3	0.28	+/-0.04	0.66	+/-0.01	0.57	+/-0.02	0.53	+/-0.01	78.3	+/-2.9	6.6	+/-0.6	5.0	+/-0.4
common 4	203	dssp	3	PHD	71.7	+/-0.7	75.8	+/-2.0	76.9	+/-2.1	60.3	+/-2.3	61.8	+/-2.4	69.1	+/-1.1	71.3	+/-0.9	67.2	+/-1.0	69.8	+/-1.7	66.7	+/-1.9	62.7	+/-1.1	4.0	+/-0.3	0.24	+/-0.04	0.61	+/-0.02	0.52	+/-0.02	0.49	+/-0.01	77.3	+/-2.9	7.8	+/-0.6	5.6	+/-0.4

subset	nprot	sots	rank	method	Q3	ERRsigQ3	Q3H%o	ERRsigQ3H%o	Q3H%p	ERRsigQ3H%p	Q3E%o	ERRsigQ3E%o	Q3E%p	ERRsigQ3E%p	Q3L%o	ERRsigQ3L%o	Q3L%p	ERRsigQ3L%p	sov	ERRsigsov	sovH	ERRsigsovH	sovE	ERRsigsovE	sovL	ERRsigsovL	BAD	ERRsigBAD	info	ERRsiginfo	corrH	ERRsigcorrH	corrE	ERRsigcorrE	corrL	ERRsigcorrL	class	ERRsigclass	contDH	ERRsigcontDH	contDE	ERRsigcontDE
Set 5			Sorted alphabetically for identical ranks!		MORE SCORES
common 5	279	dssp	1	PROF	76.3	+/-0.6	79.6	+/-1.8	82.9	+/-1.8	68.8	+/-2.3	70.1	+/-2.3	74.2	+/-0.8	74.1	+/-0.8	72.1	+/-0.9	74.3	+/-1.4	71.4	+/-1.7	67.9	+/-0.9	2.5	+/-0.2	0.35	+/-0.01	0.69	+/-0.01	0.62	+/-0.02	0.56	+/-0.01	81.7	+/-2.3	6.3	+/-0.5	4.6	+/-0.3
				PSIpred	76.1	+/-0.6	82.1	+/-1.7	82.0	+/-1.8	68.9	+/-2.3	72.1	+/-2.5	74.7	+/-0.8	73.6	+/-0.9	71.3	+/-1.0	76.8	+/-1.4	70.0	+/-1.8	67.7	+/-1.0	2.2	+/-0.2	0.36	+/-0.01	0.70	+/-0.01	0.64	+/-0.02	0.57	+/-0.01	82.1	+/-2.3	6.3	+/-0.5	4.6	+/-0.4
common 5	279	dssp	2	PHDpsi	74.2	+/-0.6	77.7	+/-1.8	80.6	+/-1.8	63.1	+/-2.2	67.4	+/-2.3	72.4	+/-0.9	71.9	+/-0.8	68.7	+/-0.9	72.3	+/-1.4	67.1	+/-1.7	64.3	+/-1.0	3.1	+/-0.3	0.28	+/-0.03	0.66	+/-0.01	0.57	+/-0.02	0.53	+/-0.01	78.1	+/-2.5	6.9	+/-0.5	5.3	+/-0.4
common 5	279	dssp	3	PHD	71.7	+/-0.6	75.8	+/-1.8	76.9	+/-1.8	60.3	+/-2.0	61.8	+/-2.1	69.3	+/-0.9	70.9	+/-0.9	67.2	+/-0.9	70.9	+/-1.5	65.5	+/-1.7	62.7	+/-0.9	4.2	+/-0.3	0.25	+/-0.03	0.61	+/-0.01	0.52	+/-0.02	0.49	+/-0.01	76.0	+/-2.6	8.1	+/-0.5	6.0	+/-0.4

Last update: Jul 6, 2001
Contact: rost@columbia.edu
WWW: http://cubic.bioc.columbia.edu/eva

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EVA summary for category sec (3)

About secondary structure prediction methods evaluated

Comparison of secondary structure prediction methods (detail level 3)

Set 1

Set 2

Set 3

Set 4

Set 5