Table 6.
Representative software tools predicting β-barrel OMPs.
| Tool | Method | Target | URL or reference |
|---|---|---|---|
| Neuwald’s | Motif searching | TMβ-strand | [261] |
| Gromiha’s | Physicochemical property, structure and statistics based | TM β-strand | [262] |
| BBF | Physicochemical property, structure and statistics based | β-barrel OMP | [263] |
| BOMP | Physicochemical property, structure and statistics based | β-barrel OMP | http://www.bioinfo.no/tools/bomp; [264] |
| transFold | Physicochemical property, structure and statistics based | TM β-barrel; residue side-chain orientations; inter-strand residue contact; strand inclination | http://bioinformatics.bc.edu/clotelab/transFold; [265] |
| HHomp | Sequence similarity searching | β-barrel OMP | http://toolkit.tuebingen.mpg.de/hhomp; [266] |
| Freeman-Wimley | Physicochemical property, structure and statistics based | TM β-barrel | http://www.tulane.edu/~biochem/WW/apps.html; [256] |
| OM-TOPO-PREDICT | NN | TM β-strand; OMP topology | http://strucbio.biologie.unikonstanz.de/-kay/om-topo-predict.html (Page not found); [267] |
| B2TMPRED | NN | TM β-strand; OMP topology | http://www.biocomp.unibo.it; [268] |
| TMBETA-NET | NN | TM β-strand | http://psfs.cbrc.jp/tmbeta-net/; [269] |
| TMBpro | NN | TM β-barrel; secondary structure; β-contacts; tertiary structure | http://www.igb.uci.edu/servers/psss.html; [270] |
| TBBPred | NN + SVM | TM β-barrel | http://www.imtech.res.in/raghava/tbbpred; [270] |
| TMbeta-SVM | SVM (sequential Aac + residue pairs) | β-barrel OMP | http://tmbeta-svm.cbrc.jp; [276] |
| PredβTM | SVM (position-specific Aac + residue pairs) | TM β-strand | http://transpred.ki.si/; [277] |
| BOCTOPUS/ BOCTOPUS2 | SVM; HMM | OMP topology | http://boctopus.cbr.su.se/; [284], [285] |
| HMMB2TMR | HMM | OMP topology | [273] |
| PROFtmb | HMM (beta-hairpin motifs) | β-barrel OMP; non-β-barrel OMP | http://www.rostlab.org/services/PROFtmb/; [274] |
| PRED-TMBB | HMM; | OMP; soluble protein | http://bioinformatics.biol.uoa.gr/PRED-TMBB; [275] |
| ConBBPRED | Consensus approaches | β-strand; OMP topology | http://bioinformatics.biol.uoa.gr/ConBBPRED; [286] |
| TMB-Hunt | k-NN | β-barrel TMP; non-β-barrel TMP | http://www.bioinformatics.leeds.ac.uk/betaBarrel; [278] |
| IDQD | Quadratic discriminant analysis | β-barrel TMP; TMH; global protein | [280] |
| TMBETADISC-RBF | Radial Basis Function (RBF) Networks | OMP | http://rbf.bioinfo.tw/~sachen/OMP.html; [281] |
| GRHCRF | Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) | OMP | http://www.biocomp.unibo.it/~savojard/biocrf-0.9.tar.gz; [282] |
| BetAware | N-to-1 Extreme Learning | β-barrel TMP | http://betaware.biocomp.unibo.it/BetAware; [255] |
| BETAWARE | N-to-1 network encoding and ELM training algorithm | β-barrel TMP | http://www.biocomp.unibo.it/~savojard/betawarecl; [283] |
| MemBrain-TMB | Statistical machine learning | β-barrel TMP | www.csbio.sjtu.edu.cn/bioinf/MemBrain-TMB; [257] |
| Koehler's | NN | β-barrel TMP; TMH | [272] |