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EVA summary for category threading, best of first 5 hits (1)

Contents

Local link to information about methods evaluated
All prediction results for threading

Common subset 1
Common subset 2
Common subset 3

All prediction results in ASCII (raw text)
Explanations of measures for prediction accuracy
For older versions of the results

About threading prediction methods evaluated

Method		Nprot	Nweek	Detailed results for method
ALL		664	270	method/index.html

3D-PSSM		484	219	method/3dpssm.html
BLAST		534	232	method/blast.html
FUGUE		564	237	method/fugue.html
Libellula		159	80	method/libellula.html
Prospect		150	73	method/prospect.html
PSI-BLAST		548	236	method/psiblast.html
SAMt99		220	137	method/samt99.html
ssearch		537	230	method/ssearch.html
Superfamily		297	130	method/superfamily.html

Comparison of threading prediction methods (detail level 1)

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:
Detail level 1 (this file) as ASCII

(...) contain standard error of a mean

subset	nprot	rank	Method	Sgnf(-lnP_MMT)	Sgnf(Z_CE)	Sgnf(Q_LG1)	Sgnf(Q_LG2)	N3.5A_Gbl%
Set 1			Sorted alphabetically for identical ranks!		MORE SCORES
common 1	15	1	3D-PSSM	10	5	10	11	30.4 (+/-6.8)
			BLAST	0	0	2	3	10.2 (+/-4.4)
			FUGUE	12	7	10	13	30.5 (+/-7.0)
			Libellula	9	5	8	11	24.2 (+/-5.8)
			Prospect	9	6	9	12	19.7 (+/-5.6)
			PSI-BLAST	4	2	4	3	14.3 (+/-4.6)
			SAMt99	7	4	6	10	27.9 (+/-7.2)
			ssearch	2	2	3	8	10.5 (+/-5.4)

subset	nprot	rank	Method	Sgnf(-lnP_MMT)	Sgnf(Z_CE)	Sgnf(Q_LG1)	Sgnf(Q_LG2)	N3.5A_Gbl%
Set 2			Sorted alphabetically for identical ranks!		MORE SCORES
common 2	66	1	3D-PSSM	44	29	26	48	34.7 (+/-3.8)
			BLAST	18	12	13	30	19.9 (+/-3.4)
			FUGUE	42	30	26	52	33.3 (+/-3.9)
			PSI-BLAST	19	10	11	25	19.1 (+/-3.1)
			SAMt99	40	26	20	46	33.6 (+/-4.0)
			ssearch	26	19	17	33	21.6 (+/-3.8)
			Superfamily	32	18	15	39	28.2 (+/-3.9)

subset	nprot	rank	Method	Sgnf(-lnP_MMT)	Sgnf(Z_CE)	Sgnf(Q_LG1)	Sgnf(Q_LG2)	N3.5A_Gbl%
Set 3			Sorted alphabetically for identical ranks!		MORE SCORES
common 3	133	1	3D-PSSM	95	57	62	103	30.9 (+/-2.6)
			BLAST	27	15	25	46	16.0 (+/-2.3)
			FUGUE	93	67	62	107	29.6 (+/-2.7)
			PSI-BLAST	46	26	28	50	19.4 (+/-2.3)
			SAMt99	81	48	47	88	29.5 (+/-2.7)
			ssearch	47	32	33	65	19.1 (+/-2.6)

Last update: Mar 5, 2004
Contact: rost@columbia.edu
WWW: http://cubic.bioc.columbia.edu/eva

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