Table 6

The available predictors, used for predicting the transmembrane strands of β-barrel outer membrane proteins.

Method

Reference

Type

TM Strands

TM Strands + Orientation

Discrimination

URL


B2TMPRED

[15]

NN

x

-

-

http://gpcr.biocomp.unibo.it/cgi/predictors/outer/pred_outercgi.cgi webcite

HMM-B2TMR (1)

[17]

HMM

x

x

-

http://gpcr.biocomp.unibo.it/biodec/ webcite (1)

OM_Topo_predict (2)

[14]

NN

x

x

-

http://strucbio.biologie.uni-konstanz.de/~kay/om_topo_predict2.html webcite (2)

PRED-TMBB

[19, 20]

HMM

x

x

x

http://bioinformatics.biol.uoa.gr/PRED-TMBB/ webcite

ProfTMB

[21]

HMM

x

x

x

http://cubic.bioc.columbia.edu/services/proftmb/ webcite

TBBpred

[22]

NN+SVM

x

-

x

http://www.imtech.res.in/raghava/tbbpred/ webcite

BETA-TM

[58]

HMM

x

x

-

http://dblab.sejong.ac.kr:8080/barrel/index.html webcite

TMBETA-NET

[16]

NN

x

-

-

http://psfs.cbrc.jp/tmbeta-net/ webcite

PSI-PRED

[62]

NN

-

-

-

http://bioinf.cs.ucl.ac.uk/psipred/ webcite


We list the name of the predictor, the reference paper, the type of the method (HMM, NN or SVM), whether it predicts the transmembrane strands, the full topology (TM strands+orientation) and if they are capable of discriminating between β-barrel membrane proteins from non-β barrel membrane proteins.

(1) HMM-B2TMR is available as a commercial demo only.

(2) The OM_Topo_predict web server was not operational, at the time when this research was conducted.

Bagos et al. BMC Bioinformatics 2005 6:7   doi:10.1186/1471-2105-6-7

Open Data