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EVA summary for category sec (3)

Contents

Local link to information about methods evaluated
All prediction results for secondary structure

Common subset 1
Common subset 2
Common subset 3
Common subset 4

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	399	58	method/index.html

APSSP	26	9	method/apssp.html
JPred	301	51	method/jpred.html
PHD	377	58	method/phd.html
PHDpsi	377	58	method/phdpsi.html
PROF0	198	38	method/prof0.html
PROF	367	56	method/prof1.html
PROF_king	273	43	method/prof_king.html
PSIpred	366	57	method/psipred.html
PSSP	319	48	method/pssp.html
SAM-T99sec	219	43	method/samt99_sec.html
SSpro	313	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: 15 proteins and 8 methods (HTML - ASCII)
- set 2: 116 proteins and 8 methods (HTML - ASCII)
- set 3: 119 proteins and 7 methods (HTML - ASCII)
- set 4: 205 proteins and 6 methods (HTML - ASCII)
- set 5: 282 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	15	dssp	1	JPred	70.0	+/-3.6	71.7	+/-12.0	84.0	+/-13.2	57.5	+/-9.2	73.5	+/-11.5	80.0	+/-2.7	69.1	+/-5.1	67.2	+/-5.5	54.5	+/-9.6	60.9	+/-8.1	68.2	+/-5.3	3.0	+/-1.2	0.26	+/-0.04	0.65	+/-0.09	0.58	+/-0.09	0.54	+/-0.06	66.7	+/-12.6	9.7	+/-1.8	9.1	+/-3.0
				PHD	70.9	+/-2.7	75.3	+/-10.3	77.4	+/-9.2	60.7	+/-9.3	62.0	+/-9.9	75.7	+/-3.5	71.7	+/-4.4	63.4	+/-3.1	61.7	+/-7.9	59.9	+/-7.4	64.9	+/-2.4	4.6	+/-1.2	0.27	+/-0.03	0.62	+/-0.08	0.52	+/-0.07	0.49	+/-0.04	73.3	+/-11.8	7.2	+/-1.7	9.4	+/-1.8
				PHDpsi	70.5	+/-2.5	77.8	+/-11.8	81.2	+/-11.1	63.6	+/-9.0	67.7	+/-10.2	74.3	+/-2.5	71.5	+/-4.3	62.8	+/-3.3	55.6	+/-8.4	65.7	+/-6.4	60.3	+/-3.4	4.0	+/-1.2	0.27	+/-0.03	0.67	+/-0.10	0.57	+/-0.07	0.53	+/-0.04	80.0	+/-10.7	6.9	+/-1.5	7.3	+/-1.7
				PROF	72.5	+/-3.1	79.5	+/-12.1	83.4	+/-12.3	68.8	+/-10.0	70.1	+/-11.0	73.8	+/-2.5	74.2	+/-4.2	69.8	+/-4.2	58.3	+/-9.6	70.7	+/-6.6	67.1	+/-4.2	3.8	+/-1.7	0.30	+/-0.03	0.70	+/-0.11	0.62	+/-0.07	0.56	+/-0.04	93.3	+/-6.7	7.1	+/-1.8	6.9	+/-2.1
				PSIpred	72.9	+/-2.1	81.3	+/-9.5	82.3	+/-9.6	68.8	+/-11.6	71.2	+/-11.4	70.7	+/-3.1	74.7	+/-4.2	67.9	+/-4.6	72.1	+/-8.0	65.6	+/-8.7	63.1	+/-4.3	0.9	+/-0.3	0.31	+/-0.04	0.70	+/-0.08	0.63	+/-0.09	0.57	+/-0.07	86.7	+/-9.1	7.9	+/-2.4	4.4	+/-1.8
				SAM-T99sec	71.8	+/-2.6	83.6	+/-9.4	78.0	+/-8.6	61.9	+/-9.5	75.2	+/-11.7	70.8	+/-3.6	74.5	+/-4.4	64.9	+/-4.0	68.8	+/-7.1	63.7	+/-7.8	62.2	+/-4.2	2.3	+/-0.7	0.29	+/-0.04	0.68	+/-0.07	0.61	+/-0.08	0.54	+/-0.06	86.7	+/-9.1	8.5	+/-2.1	6.0	+/-2.4
common 1	15	dssp	2	APSSP	62.6	+/-2.8	63.5	+/-10.2	67.9	+/-9.9	32.5	+/-6.0	48.9	+/-9.2	76.3	+/-3.2	63.7	+/-4.6	49.9	+/-3.8	45.7	+/-8.3	42.3	+/-9.0	56.3	+/-3.7	6.2	+/-1.3	0.14	+/-0.02	0.45	+/-0.08	0.28	+/-0.10	0.37	+/-0.05	73.3	+/-11.8	7.1	+/-1.8	15.1	+/-2.8
				PSSP	62.8	+/-2.8	63.3	+/-8.9	71.2	+/-9.2	54.9	+/-9.1	48.1	+/-8.9	67.5	+/-3.0	66.2	+/-5.1	53.0	+/-3.1	57.2	+/-8.3	54.5	+/-8.1	53.3	+/-2.9	6.0	+/-1.6	0.18	+/-0.03	0.48	+/-0.08	0.38	+/-0.09	0.38	+/-0.05	66.7	+/-12.6	7.9	+/-1.5	11.1	+/-2.2

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	116	dssp	1	JPred	75.6	+/-0.9	71.7	+/-2.8	84.0	+/-3.1	57.5	+/-3.1	73.5	+/-3.7	80.6	+/-1.4	69.2	+/-1.2	69.1	+/-1.5	69.8	+/-2.5	65.8	+/-2.7	67.1	+/-1.6	1.7	+/-0.2	0.34	+/-0.01	0.65	+/-0.02	0.58	+/-0.03	0.54	+/-0.02	78.4	+/-3.8	6.8	+/-0.7	5.4	+/-0.5
				PROF	76.4	+/-0.9	79.5	+/-2.6	83.4	+/-2.7	68.8	+/-3.5	70.1	+/-3.5	72.7	+/-1.5	74.8	+/-1.2	71.6	+/-1.4	74.1	+/-2.1	71.1	+/-2.7	67.4	+/-1.6	2.1	+/-0.2	0.35	+/-0.01	0.70	+/-0.02	0.62	+/-0.02	0.56	+/-0.02	82.8	+/-3.5	6.1	+/-0.7	4.0	+/-0.4
				PSIpred	76.5	+/-1.0	81.3	+/-2.6	82.3	+/-2.7	68.8	+/-3.5	71.2	+/-3.7	74.6	+/-1.2	74.5	+/-1.2	71.7	+/-1.5	77.1	+/-2.2	68.8	+/-2.8	68.3	+/-1.5	2.2	+/-0.3	0.36	+/-0.02	0.70	+/-0.02	0.63	+/-0.03	0.57	+/-0.02	83.6	+/-3.5	5.9	+/-0.7	4.4	+/-0.5
				SAM-T99sec	76.3	+/-0.9	83.6	+/-2.7	78.0	+/-2.6	61.9	+/-3.2	75.2	+/-3.7	70.6	+/-1.8	74.8	+/-1.5	71.0	+/-1.4	75.2	+/-2.2	69.2	+/-2.6	65.2	+/-1.8	1.6	+/-0.2	0.35	+/-0.01	0.68	+/-0.02	0.61	+/-0.02	0.54	+/-0.02	81.9	+/-3.6	6.5	+/-0.8	4.4	+/-0.5
				SSpro	76.1	+/-1.0	80.5	+/-2.6	81.7	+/-2.7	63.2	+/-3.3	71.8	+/-3.7	75.2	+/-1.3	74.4	+/-1.2	69.3	+/-1.6	75.2	+/-2.2	67.5	+/-2.7	66.2	+/-1.7	2.2	+/-0.3	0.35	+/-0.02	0.69	+/-0.02	0.60	+/-0.02	0.56	+/-0.02	80.2	+/-3.7	6.7	+/-0.8	5.4	+/-0.6
common 2	116	dssp	2	PHDpsi	74.5	+/-0.9	77.8	+/-2.7	81.2	+/-2.8	63.6	+/-3.3	67.7	+/-3.4	71.0	+/-1.5	73.0	+/-1.2	68.7	+/-1.3	72.2	+/-2.3	67.7	+/-2.7	63.8	+/-1.6	2.7	+/-0.3	0.24	+/-0.07	0.67	+/-0.02	0.57	+/-0.03	0.53	+/-0.02	80.2	+/-3.7	6.7	+/-0.7	4.8	+/-0.5
common 2	116	dssp	3	PHD	72.0	+/-1.0	75.3	+/-2.7	77.4	+/-2.8	60.7	+/-3.1	62.0	+/-3.2	67.8	+/-1.4	71.9	+/-1.3	67.4	+/-1.3	70.8	+/-2.3	66.8	+/-2.7	62.3	+/-1.5	3.5	+/-0.3	0.21	+/-0.07	0.62	+/-0.02	0.52	+/-0.03	0.49	+/-0.01	80.2	+/-3.7	7.8	+/-0.8	5.5	+/-0.6
common 2	116	dssp	4	PSSP	63.7	+/-1.0	63.3	+/-2.5	71.2	+/-2.8	54.9	+/-2.8	48.1	+/-2.7	64.9	+/-1.3	64.5	+/-1.3	57.7	+/-1.2	58.4	+/-2.2	61.9	+/-2.6	56.5	+/-1.5	6.4	+/-0.5	0.19	+/-0.01	0.48	+/-0.02	0.38	+/-0.03	0.38	+/-0.02	72.4	+/-4.2	9.6	+/-0.9	8.2	+/-0.6

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	119	dssp	1	JPred	75.5	+/-0.9	71.7	+/-2.8	84.0	+/-3.0	57.5	+/-3.0	73.5	+/-3.6	80.7	+/-1.3	69.2	+/-1.2	69.1	+/-1.4	69.2	+/-2.5	66.2	+/-2.7	67.4	+/-1.5	1.7	+/-0.2	0.34	+/-0.01	0.65	+/-0.02	0.58	+/-0.02	0.54	+/-0.02	79.0	+/-3.8	6.9	+/-0.7	5.3	+/-0.5
				PHDpsi	74.6	+/-0.9	77.8	+/-2.6	81.2	+/-2.8	63.6	+/-3.2	67.7	+/-3.4	71.1	+/-1.4	73.2	+/-1.2	68.9	+/-1.3	72.2	+/-2.2	68.0	+/-2.6	64.2	+/-1.6	2.7	+/-0.3	0.25	+/-0.07	0.67	+/-0.02	0.57	+/-0.02	0.53	+/-0.02	80.7	+/-3.6	6.6	+/-0.7	4.8	+/-0.5
				PROF	76.3	+/-0.9	79.5	+/-2.5	83.4	+/-2.6	68.8	+/-3.4	70.1	+/-3.4	72.8	+/-1.4	74.7	+/-1.2	71.7	+/-1.3	73.7	+/-2.1	71.2	+/-2.6	67.6	+/-1.5	2.1	+/-0.2	0.34	+/-0.01	0.70	+/-0.02	0.62	+/-0.02	0.56	+/-0.02	83.2	+/-3.4	6.1	+/-0.7	4.0	+/-0.4
				PSIpred	76.3	+/-0.9	81.3	+/-2.6	82.3	+/-2.7	68.8	+/-3.5	71.2	+/-3.6	74.6	+/-1.2	74.4	+/-1.2	71.8	+/-1.4	76.6	+/-2.2	69.1	+/-2.7	68.4	+/-1.5	2.2	+/-0.3	0.36	+/-0.02	0.70	+/-0.02	0.63	+/-0.03	0.57	+/-0.02	84.0	+/-3.4	5.8	+/-0.6	4.4	+/-0.5
				SAM-T99sec	76.2	+/-0.9	83.6	+/-2.7	78.0	+/-2.5	61.9	+/-3.1	75.2	+/-3.6	70.9	+/-1.7	74.7	+/-1.4	71.1	+/-1.3	74.8	+/-2.2	69.4	+/-2.5	65.5	+/-1.7	1.6	+/-0.2	0.35	+/-0.01	0.68	+/-0.02	0.61	+/-0.02	0.54	+/-0.02	82.4	+/-3.5	6.5	+/-0.8	4.3	+/-0.5
				SSpro	76.1	+/-0.9	80.5	+/-2.5	81.7	+/-2.6	63.2	+/-3.3	71.8	+/-3.6	75.4	+/-1.3	74.4	+/-1.1	69.4	+/-1.6	74.8	+/-2.1	67.9	+/-2.7	66.5	+/-1.6	2.2	+/-0.3	0.35	+/-0.02	0.69	+/-0.02	0.60	+/-0.02	0.56	+/-0.02	80.7	+/-3.6	6.6	+/-0.7	5.3	+/-0.5
common 3	119	dssp	2	PHD	72.1	+/-0.9	75.3	+/-2.6	77.4	+/-2.7	60.7	+/-3.0	62.0	+/-3.1	68.0	+/-1.4	71.9	+/-1.2	67.5	+/-1.3	70.7	+/-2.2	67.1	+/-2.6	62.6	+/-1.5	3.5	+/-0.3	0.21	+/-0.07	0.62	+/-0.02	0.52	+/-0.02	0.49	+/-0.01	80.7	+/-3.6	7.8	+/-0.8	5.5	+/-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	205	dssp	1	PROF	76.3	+/-0.6	79.5	+/-2.0	83.4	+/-2.0	68.8	+/-2.6	70.1	+/-2.6	74.4	+/-1.0	74.2	+/-0.8	72.1	+/-0.9	73.5	+/-1.6	71.4	+/-1.9	68.4	+/-1.1	2.3	+/-0.2	0.35	+/-0.01	0.70	+/-0.01	0.62	+/-0.02	0.56	+/-0.01	81.5	+/-2.7	6.0	+/-0.5	4.1	+/-0.3
				PSIpred	76.2	+/-0.7	81.3	+/-1.9	82.3	+/-2.0	68.8	+/-2.6	71.2	+/-2.7	75.3	+/-0.9	73.9	+/-0.9	71.6	+/-1.1	76.4	+/-1.6	69.8	+/-2.0	68.4	+/-1.1	2.3	+/-0.2	0.36	+/-0.01	0.70	+/-0.02	0.63	+/-0.02	0.57	+/-0.01	81.0	+/-2.7	5.8	+/-0.5	4.6	+/-0.4
				SSpro	75.9	+/-0.7	80.5	+/-1.9	81.7	+/-2.0	63.2	+/-2.4	71.8	+/-2.7	75.8	+/-0.9	73.8	+/-0.9	70.4	+/-1.1	74.3	+/-1.6	68.9	+/-1.9	67.3	+/-1.2	2.4	+/-0.2	0.35	+/-0.01	0.69	+/-0.01	0.60	+/-0.02	0.56	+/-0.01	82.0	+/-2.7	6.1	+/-0.5	5.1	+/-0.4
common 4	205	dssp	2	JPred	74.7	+/-0.6	71.7	+/-2.1	84.0	+/-2.2	57.5	+/-2.3	73.5	+/-2.7	82.1	+/-0.9	68.3	+/-0.9	69.2	+/-1.1	69.2	+/-1.8	66.4	+/-2.0	68.3	+/-1.1	2.3	+/-0.2	0.33	+/-0.01	0.65	+/-0.02	0.58	+/-0.02	0.54	+/-0.01	76.6	+/-3.0	7.8	+/-0.5	5.7	+/-0.4
				PHDpsi	74.4	+/-0.6	77.8	+/-2.0	81.2	+/-2.1	63.6	+/-2.4	67.7	+/-2.5	72.4	+/-1.0	72.6	+/-0.8	69.0	+/-0.9	71.9	+/-1.7	68.1	+/-1.9	64.8	+/-1.1	2.9	+/-0.3	0.28	+/-0.04	0.67	+/-0.01	0.57	+/-0.02	0.53	+/-0.01	78.0	+/-2.9	6.6	+/-0.5	5.0	+/-0.4
common 4	205	dssp	3	PHD	71.7	+/-0.7	75.3	+/-2.0	77.4	+/-2.1	60.7	+/-2.3	62.0	+/-2.4	69.1	+/-1.1	71.4	+/-0.9	67.2	+/-1.0	70.0	+/-1.7	66.8	+/-1.9	62.7	+/-1.1	4.0	+/-0.3	0.24	+/-0.04	0.62	+/-0.02	0.52	+/-0.02	0.49	+/-0.01	77.1	+/-2.9	7.8	+/-0.6	5.7	+/-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	282	dssp	1	PROF	76.3	+/-0.6	79.5	+/-1.8	83.4	+/-1.8	68.8	+/-2.3	70.1	+/-2.3	74.2	+/-0.8	74.1	+/-0.8	72.1	+/-0.8	74.5	+/-1.4	71.3	+/-1.6	67.9	+/-0.9	2.5	+/-0.2	0.35	+/-0.01	0.70	+/-0.01	0.62	+/-0.02	0.56	+/-0.01	81.9	+/-2.3	6.3	+/-0.5	4.6	+/-0.3
				PSIpred	76.1	+/-0.6	81.3	+/-1.7	82.3	+/-1.8	68.8	+/-2.3	71.2	+/-2.4	74.7	+/-0.8	73.6	+/-0.8	71.4	+/-1.0	77.0	+/-1.4	70.0	+/-1.7	67.8	+/-1.0	2.2	+/-0.2	0.36	+/-0.01	0.70	+/-0.01	0.63	+/-0.02	0.57	+/-0.01	82.3	+/-2.3	6.3	+/-0.5	4.6	+/-0.4
common 5	282	dssp	2	PHDpsi	74.1	+/-0.6	77.8	+/-1.8	81.2	+/-1.8	63.6	+/-2.1	67.7	+/-2.3	72.3	+/-0.9	71.9	+/-0.8	68.7	+/-0.9	72.5	+/-1.4	67.1	+/-1.7	64.3	+/-1.0	3.1	+/-0.3	0.28	+/-0.03	0.67	+/-0.01	0.57	+/-0.02	0.53	+/-0.01	77.7	+/-2.5	6.9	+/-0.5	5.3	+/-0.4
common 5	282	dssp	3	PHD	71.7	+/-0.6	75.3	+/-1.8	77.4	+/-1.8	60.7	+/-2.0	62.0	+/-2.1	69.2	+/-0.9	70.9	+/-0.9	67.2	+/-0.9	71.0	+/-1.5	65.5	+/-1.7	62.7	+/-0.9	4.2	+/-0.3	0.25	+/-0.03	0.62	+/-0.01	0.52	+/-0.02	0.49	+/-0.01	75.5	+/-2.6	8.1	+/-0.5	6.1	+/-0.4

Last update: Jul 4, 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