Table 2.
Features of the most common computational tools available for the prediction of trans-membrane (TM) domains.
| Tools | Important features | Website/reference |
|---|---|---|
| TMHMM Server v. 2.0 | Predicts trans-membrane (TM) domains; a common mistake by the program consists in reversing the direction of proteins with one TM segment | www.cbs.dtu.dk/services/TMHMM/ |
| TMpred | Predicts TM regions and orientation. The TMpred program makes a prediction of membrane-spanning regions and their orientation | www.ch.embnet.org |
| Hofman, 1993 | ||
| TMbase | Offers a good database of TM proteins and their helical membrane- spanning domains; TMbase was originally meant as a tool for analyzing the properties of TM proteins | www.ch.embnet.org |
| Hofman, 1993 | ||
| HMMTOP | Serves as automatic server for predicting TM helices and topology of proteins | Tusnady and Simon, 2001 www.enzim.hu/hmmtop/ |
| PredictProtein | Predicts secondary structures | Rost et al., 2004 www.predictprotein.org/ |
| SOSUI | Classifies and predicts secondary structures of membrane proteins | http://harrier.nagahama-i-bio.ac.jp/sosui/ |
| TopPred 1.10 | Predicts topology of membrane proteins | http://mobyle.pasteur.fr/cgi-bin/portal.py?\#forms::toppred |
| DAS-TMfilter server | Filters false positive TM protein predictions | http://mendel.imp.ac.at/sat/DAS/DAS.html |
| CCTOP (Consensus Constrained TOPology prediction) | Performs TM topology predictions | http://cctop.enzim.ttk.mta.hu/ |
| MetaTM | Predicts TM topologies through a consensus method | Klammer et al., 2009 http://metatm.sbc.su.se/ |
| MINNOU | Predicts membrane proteins with and without explicit use of hydropathy profiles and alignments | http://minnou.cchmc.org/ |
| PHDhtm | Predicts the location of helical TM segments in integral membrane proteins through a neural network system | https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_htm.html |
| Phobius | Combines TM topology and signal peptide predictions | Käll et al., 2007 |
| http://phobius.sbc.su.se/poly.html | ||
| PRED-TMR | Refines a standard hydrophobicity with a detection of potential edges | Pasquier et al., 1999 |
| http://athina.biol.uoa.gr/ | ||
| SCAMPI | Uses position-specific amino acid contributions to the free energy of membrane insertion and also uses the current best statistics-based topology predictors | Bernsel et al., 2008 http://scampi.cbr.su.se/ |
| SOMRuler | Offers an interpretable TM helices predictor | Yu et al., 2011 www.csbio.sjtu.edu.cn/bioinf/SOMRuler/ |
| ConPred | Predicts TM topology based on a consensus approach by combining the results of several methods | Arai et al., 2004 |
| http://bioinfo.si.hirosaki-u.ac.jp/ConPred2/ | ||
| TMBB-DB | Compiles the predictions made by the Freeman–Wimley algorithm | http://beta-barrel.tulane.edu/ |
| TMalphaDB | Quantifies the structural distortion induced by a sequence motif in alpha TM segments | http://lmc.uab.cat/TMalphaDB/ |
| TMexpo | Predicts rotational preferences of TM helices to facilitate structural modeling. TMexpo calculates rotational angles of TMHs based on the predicted relative accessible surface area | http://bio-cluster.iis.sinica.edu.tw/TMexpo/ |
| TMMOD | Uses an improved hidden Markov model for the identification and topology prediction of TM proteins | http://liao.cis.udel.edu/website/servers/TMMOD/scripts/frame.php?p=submit |
| Asymmetric Ez | Assesses the energy and positions of protein sequences or structures in and on the membrane through a knowledge-based potential | http://ez.degradolab.org/ez/ |