Table 2: Epitope prediction or reevaluation on accessible servers.

ProgramsPurposeTools or procedures of evaluationInputOutputInternet accessibilityReferences

Epitope prediction

MimoDB 2.0Mimotope databaseMySQL relational databaseaccording to menuStructures visualization, alignments, and so forthhttp://immunet.cn/mimodb/[105]
MimoProMaps a group of mimotopes back to a source antigen so as to locate the interacting epitope on the antigenBranch and bound optimization (analysis of overlapping patches on the surface of a protein)PDB identifier mimotope sequencesScore + 3D location in antigenhttp://informatics.nenu.edu.cn/MimoPro/[108]
ViPRVirus pathogen databaseIntegration of various resourcesaccording to menuStructures, annotations, and so forthhttp://www.viprbrc.org/[140]
MetaMHCPrediction of MHC binding epitopesmeta-approachQSFour metapredictor scores including MetaSVMp scorehttp://www.biokdd.fudan.edu.cn/Service/MetaMHC.html[141]
EpitopiaPrediction of B-cell epitopes *MLA
*MLA + 3D + SA
*QS
*PDB ACF
Immunogenicity score + probability score + color scale record on QShttp://epitopia.tau.ac.il[115]
ElliProNew structure-based tool for the prediction of antibody epitopes3D + SA + flx + antigenicity *QS
*PDB ACF
Score + visualized epitope 3D structure and 3D locationhttp://tools.immuneepitope.org/tools/ElliPro[114]
MHCPredPrediction of class II mouse MHC peptide binding affinityISC-PLS, SYBYL software packageQSBinding affinity (pIC50)http://www.jenner.ac.uk/MHCPred[129]

Stable epitopes and vaccines

BayesBSVM-based prediction of linear B-cell epitopes using Bayes Feature ExtractionResidue conservation + position-specific residue propensitiesQSResidue epitope propensity scorehttp://www.immunopred.org/bayesb/index.html[120]
OptiTopeSelection of optimal peptides for epitope-based vaccinesMultistep parallel evaluationMSA of Ag
list of ES
table: ES, ES related MHC
Fraction of overall immunogenicity covered MHChttp://www.epitoolkit.org/optitope[142]
PVSPVS returns a variability-masked sequence, which can be submitted to the RANKPEP server to predict conserved T-cell epitopes.3D visualization of MSA derived sequence variability “per site”PDB ACF3D map of variability fragments with no variable residues and their 3D location in antigenhttp://imed.med.ucm.es/PVS/[143]
PEPVACPrediction of MHC I; server can also identify conserved and promiscuous MHC I ligandsPSSM, distance matrix, phylogenic clustering algorithmGenome, HLA-supertypesSelected peptide sequences scorehttp://immunax.dfci.harvard.edu/PEPVAC/[144]
RANKPEPPrediction of MHC I and MHC II ligandsProfile comparisonGenome, HLA-supertypes, QSSelected peptide sequences scorehttp://www.mifoundation.org/Tools/rankpep.html[145, 146]

*Independent alternatives; Ag: antigen; BFE: Bayes Feature Extraction; flx: flexibility; ES: epitope sequences; HLA: human leukocyte antigens (human MHC); ISC-PLS: iterative self-consistent partial-least-squares based additive method; MHC: alleles of major histocompatibility antigens; MLA: machine learning algorithm; MSA: multiple sequence alignment; PDB: protein data bank; PDB ACF: PDB-derived atom coordinate file; QS: query sequence(s); SA: solvent accessibility; SVM: support vector machines.