bioinformatics tools for epitope prediction

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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.

Server nameLinkPredictive server for MHCI                 MHC II   Method
EpiJen algorithm
BIMAS coefficient tables
ProPred I matrix
ProPred matrix
MHCPred method
MHC2Pred method
NetMHC based method
PREDEP coefficient tables
SVMHC method
IEDB binding and SMM method
EpiVax algorithm
MMBPred matrix
nHLAPred Neural Networks
KISS based method
IMTECH matrix

Table 2. Predictive server for TAP binding epitopes and CTL

Server nameLinkDescriptionPredictive method
EpiJen server for TAP binding epitopesMulti-step algorithm
TAP Pred server for TAP binding epitopesSVM method
WAPP server for TAP binding epitopesSVM method
CTLPred server for CTLSVM and ANN method
NetCTLPan server for CTLMulti-step algorithm

Table 3. Comprehensive list of B cell epitope prediction servers.

Server nameLinkType
Bcepred of continuous B-cell epitopes
BepiPred of continuous B-cell epitopes
ABCPred of continuous B-cell epitopes
BEST of continuous B-cell epitopes
EPCES of discontinuous B-cell epitopes
Discotope of discontinuous B-cell epitopes
BEPro (PEPITO) of discontinuous B-cell epitopes
SEPPA of discontinuous B-cell epitopes
EpiSearch of discontinuous B-cell epitopes
MimoPro of discontinuous B-cell epitopes
MIMOX of discontinuous B-cell epitopes
Pep-3D-Search of discontinuous B-cell epitopes
Epitopia of continuous and discontinuous B-cell epitopes
PepSurf of continuous and discontinuous B-cell epitopes
ElliPro 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.

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