BMC Bioinformatics

Table 2 Sensitivity benchmark results for predictions of families of membrane channels

From: A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions

	Channel structure family
Prediction Method	(1) FNT	(2) Amt/Rh	(3) Aquaporin	(4) Gap junction	(5) K⁺channel	(6) Urea transport	(7) Other
DAS1997 (strict)	90	93	80	100	89	83	92
HMMTOP (in TOPCONS-single)	86	99	75	100	80	83	97
HMMTOP2	86	99	75	100	80	83	97
MemBrain	100	93	89	100	92	75	92
MEMSAT (in TOPCONS-single)	86	99	84	100	74	83	95
MEMSAT-SVM	86	97	100	100	86	83	95
MEMSAT3	86	100	74	100	70	83	92
OCTOPUS	86	100	77	100	89	83	100
OCTOPUS (in TOPCONS)	86	97	75	100	81	83	97
Philius	86	100	75	100	83	75	89
PolyPhobius	86	100	73	100	86	83	97
PRO-TMHMM (in TOPCONS)	90	99	75	100	80	83	100
PRODIV-TMHMM (in TOPCONS)	86	100	75	100	91	83	100
SCAMPI-multi (in TOPCONS)	86	97	75	100	81	83	97
SVMtop	86	100	81	100	76	75	92
TMHMM2	86	99	75	100	75	83	89
TMMOD	86	100	75	100	79	75	84
TOPCONS	86	99	75	100	82	83	97
TOPCONS-single	86	99	75	100	76	83	97
VALPRED2	95	97	91	100	96	75	100

Each prediction method's score is given for the channel structure family benchmark data subset as specified in Table 4. The benchmark server metric used is “Qhtm %obs”. The highest score for each family is marked in bold. Results for prediction methods that did not obtain a highest score for any of these specialised channel benchmarks except the Gap Junction benchmark (for which all methods except OPM (19,0) scored 100%) have been omitted.

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ISSN: 1471-2105

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