bioinformatics tools for epitope prediction
Bioinformatics approaches play a critical role on analyzing multiple genomes to select the protective epitopes in silico. It is conceived that cocktails of defined epitopes or chimeric protein arrangements, including the target epitopes, may provide a rationale design capable to elicit convenient humoral or cellular immune responses. Here we presents a comprehensive compilation of the most advantageous online immunological software and searchable, in order to facilitate the design and development of vaccines. An outlook on how these tools are supporting vaccine development is presented.
Table 1. Comprehensive list of T cell epitope prediction servers.
Table 2. Predictive server for TAP binding epitopes and CTL
| Server name | Link | Description | Predictive method |
|---|---|---|---|
| EpiJen | http://www.ddg-pharmfac.net/epijen/EpiJen/EpiJen.htm | Predictive server for TAP binding epitopes | Multi-step algorithm |
| TAP Pred | http://www.imtech.res.in/raghava/tappred/ | Predictive server for TAP binding epitopes | SVM method |
| WAPP | http://abi.inf.uni-tuebingen.de/Services/WAPP/information | Predictive server for TAP binding epitopes | SVM method |
| CTLPred | http://www.imtech.res.in/raghava/ctlpred/ | Predictive server for CTL | SVM and ANN method |
| NetCTLPan | http://www.cbs.dtu.dk/services/NetCTLpan/ | Predictive server for CTL | Multi-step algorithm |
Table 3. Comprehensive list of B cell epitope prediction servers.
| Server name | Link | Type |
|---|---|---|
| Bcepred | http://www.imtech.res.in/raghava/bcepred/ | Prediction of continuous B-cell epitopes |
| BepiPred | http://www.cbs.dtu.dk/services/BepiPred/ | Prediction of continuous B-cell epitopes |
| ABCPred | http://www.imtech.res.in/raghava/abcpred/ | Prediction of continuous B-cell epitopes |
| BEST | http://biomine.ece.ualberta.ca/BEST/ | Prediction of continuous B-cell epitopes |
| EPCES | http://sysbio.unl.edu/services/EPCES/ | Prediction of discontinuous B-cell epitopes |
| Discotope | http://www.cbs.dtu.dk/services/DiscoTope/ | Prediction of discontinuous B-cell epitopes |
| BEPro (PEPITO) | http://pepito.proteomics.ics.uci.edu/ | Prediction of discontinuous B-cell epitopes |
| SEPPA | http://lifecenter.sgst.cn/seppa/index.php | Prediction of discontinuous B-cell epitopes |
| EpiSearch | http://curie.utmb.edu/episearch.html | Prediction of discontinuous B-cell epitopes |
| MimoPro | http://informatics.nenu.edu.cn/MimoPro | Prediction of discontinuous B-cell epitopes |
| MIMOX | http://immunet.cn/mimox/ | Prediction of discontinuous B-cell epitopes |
| Pep-3D-Search | http://kyc.nenu.edu.cn/Pep3DSearch | Prediction of discontinuous B-cell epitopes |
| Epitopia | http://epitopia.tau.ac.il/ | Prediction of continuous and discontinuous B-cell epitopes |
| PepSurf | http://pepitope.tau.ac.il | Prediction of continuous and discontinuous B-cell epitopes |
| ElliPro | http://tools.immuneepitope.org/tools/ElliPro/iedb_input | Prediction of continuous and discontinuous B-cell epitopes |
Reference: An overview of bioinformatics tools for epitope prediction: implications on vaccine development. J Biomed Inform. 2015 Feb;53:405-14. doi: 10.1016/j.jbi.2014.11.003. Epub 2014 Nov 10.