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Epitope (B cell & T-cell)

There is a tremendous change in strategy of designing vaccines, it is moving from minimisation to micro-minimization (whole pathogen to antigen to antigenic peptides). This server list severs developed for predicting compete path of antigen processing (endogenous & exogenous). It include methods for predicting; i) MHC or HLA binders, ii) helper T-cell epitopes, iii) CTL epitopes, iv) TAP binders.

Webservers for predicting epitopes  (Raghava's Group)

  1. ABCpred: Mapping of B-cell epitope(s) in an antigen sequence, using artificial neural network.
  2. Ab-Affi: Computer program for calculating affinity of a monoclonal antibody using non-competitive ELISA.
  3. BCEpred: Prediction of linear B-cell epitopes, using Physico-chemical properties.
  4. BCIpep: Collection & compilation of B-cell epitopes from literature.
  5. BTEVAL: Evaluation of beta-turns prediction methods.
  6. Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
  7. CBTOPE: Conformational B-cell Epitope prediction.
  8. ELISAeq: Computer program for determining the concentration of antibody/antigen from ELISA data.
  9. IgPred: Prediction of antibody specific B-cell epitope.
  10. LBtope: A server for predicting linear B-cell epitopes.
  11. mhc: Matrix Optimization Technique for Predicting MHC binding Core.
  12. mhcbench: Evaluation of MHC Binding Peptide Prediction Algorithms.
  13. mhc2pred:SVM based method for prediction of promiscuous MHC class II binders.
  14. MHCBN: A database od Major Histocompatibility Complex (MHC) Binding,Non-binding peptides.
  15. MHCBN4: A database of MHC/TAP binding peptides and T-cell epitopes.
  16. MtbVeb: A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
  17. MycoTb: A software for managing mycobacterium tuberculosis.
  18. Pcleavage: Identification of protesosomal cleavage sites in a protein sequence. 
  19. PolysacDB:  A comprehensive Database of microbial Polysaccharide antigens and their antibodies.
  20. ProPred: A webserver to  predict MHC Class-II binding regions in an antigen sequence.
  21. ProPred-1: Prediction of  promiscuous MHC Class-I binders.
  22. TAPPred: A webserver for predicting binding affinity of peptides toward the TAP transporter.
  23. ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. AntiInflam: Prediction of anti-inflammatory proteins/peptides: an insilico approach.
  2. BCPRED:  A novel method for predicting linear B-cell epitopes using the subsequence kernel.
  3. BepiPred: BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures.
  4. BEpro: BEPro, formerly known as PEPITO, which utilizes amino acid propensity scores, solvent accessibility and side-chain orientations quantified by half-sphere exposure in a linear regression.
  5. CEP: a conformational epitope prediction server.
  6. dbDiarrhea: the database of pathogen proteins and vaccine antigens from diarrheal pathogens.
  7. Discotope: Used for the prediction of discontinuous B cell epitopes from protein 3D structures using surface accessibility and a novel epitope propensity score of residues
  8. ElliPro: Used for prediction and analysis of antibody epitopes in a protein structure.
  9. EpiJen: It is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes.
  10. EpiPred: Method to identify the epitope region on the antigen, given the structures of the antibody and the antigen.
  11. Epitopia: Web-based tool that aims to predict immunogenic regions in either a protein three-dimensional structure or a linear sequence.
  12. EPMeta: novel server applications for discontinuous epitope prediction.
  13. EPSVR: novel server applications for discontinuous epitope prediction.
  14. HLaffy: Estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials.
  15. IEDB analysis: This site provides a collection of tools for the prediction and analysis of immune epitopes.
  16. MAPPP : Prediction of potential antigenic epitopes presented on the cell surface by MHC I molecules to CD8 positive T lymphocytes.
  17. MHCPred: A server for quantitative prediction of peptide–MHC binding.
  18. MULTIPRED2: It is used to screen peptide that binds to multiple alleles belonging to HLA class I and class II DR super types.
  19. NetChop: Produces neural network predictions for cleavage sites of the human proteasome.
  20. NetCTL: Web-based tool designed for predicting human CTL epitopes in any given protein.
  21. NetMHC: NetMHC-4.0 is used for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment.
  22. NetMHCPan: MHC Class I interaction predictions integrating eluted ligand and peptide binding affinity data
  23. NetMHCII: NetMHCII 2.3 server predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks.
  24. NetMHCIIPan: NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules.
  25. PAProC: Prediction algorithm for proteasomal cleavages. Also linked to diseases like Alzheimer's , Parkinson's and Huntington's disease.
  26. PEASE (Predicting Epitopes using Antibody Sequence): Predicts antibody-specific epitopes using sequence information of the antibody.
  27. ProInflam: A webserver for the prediction of proinflammatory antigenicity of peptides and proteins.
  28. RANKPEP: Used for both class I and II MHC, based on the comparison of sequence similarities, using position-specific scoring matrices method.
  29. SVMTriP: It is a method to predict linear antigenic epitopes. Support Vector Machine has been utilized by combining the Tri-peptide similarity and Propensity scores (SVMTriP).
  30. SYFPEITHI: It is a database for MHC ligands and peptide motifs.