Biomedical Engineering Reference
In-Depth Information
TMBs, and it could discriminate with the accuracy of 94.2% in a set of 1,088
proteins. This will also have the ability of correctly excluding 1,612 proteins
belonging to 30 major folds of globular proteins with the accuracy of 99%. In
addition, we have developed a method based on radial basis function (RBF)
networks and position-specific scoring matrices (PSSM) profiles, which enhanced
the accuracy of discriminating 268 TMBs and 1,045 non-TMBs to an accuracy of
96.4% [
57
].
The comparison of several statistical and machine-learning techniques for dis-
criminating TMBs is presented in Table
3
. We noticed that the accuracy is remark-
ably higher with machine-learning techniques than with statistical methods.
Further, the statistical methods could correctly identify the TMBs, whereas the
performance of machine-learning techniques is better for excluding globular and
TMH proteins than identifying TMBs.
The online resources available for discriminating
b
-barrel membrane proteins
are listed in Table
4
.
Table 3 Comparison between statistical methods and machine learning techniques for discrimi-
nating
b
-barrel membrane proteins
Method
Parameters
Sensitivity
Specificity
Accuracy
Reference
Statistical
AAC
89
79
83
[
43
]
Statistical
Residue pairs
95
79
86
[
44
]
Statistical
Motifs
96
86
90
[
45
]
SVM
18 AA + 10 pairs
91
95
94
[
56
]
NN
49 Properties
81
98
94
[
51
]
RBF
PSSM profiles
89
98
96
[
57
]
18 AA: All amino acids except Ala and Glu
10 pairs: QA, DF, DA, KK, EF, NK, DR, YN, FF and LI
AAC
amino acid composition
Table 4 Web servers for transmembrane strand prediction
Name
URL
PRED-TMBB
http://bioinformatics.biol.uoa.gr/PRED-TMBB
TMB-HUNT
www.bioinformatics.leeds.ac.uk/betaBarrel
TMBETA-DISC
http://psfs.cbrc.jp/tmbetadisc/
TMBETA-SVM
http://tmbeta-svm.cbrc.jp/
TMETADISC-RBF
http://rbf.bioinfo.tw/~sachen/OMP.html
ProfTMB
http://cubic.bioc.columbia.edu/services/proftmb/
TBBpred
http://www.imtech.res.in/raghava/tbbpred/
TMBETA-NET
http://psfs.cbrc.jp/tmbeta-net/
ConBBPRED
http://bioinformatics.biol.uoa.gr/ConBBPRED/
TMBpro
http://www.igb.uci.edu/servers/psss.html
TMBETAPRED-RBF
http://rbf.bioinfo.tw/~sachen/tmrbf.html
Freeman-Wimley algorithm
http://www.tulane.edu/~biochem/WW/apps.html
