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)
- ABCpred: Mapping of B-cell epitope(s) in an antigen sequence, using artificial neural network.
- Ab-Affi: Computer program for calculating affinity of a monoclonal antibody using non-competitive ELISA.
- BCEpred: Prediction of linear B-cell epitopes, using Physico-chemical properties.
- BCIpep: Collection & compilation of B-cell epitopes from literature.
- BTEVAL: Evaluation of beta-turns prediction methods.
- Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
- CBTOPE: Conformational B-cell Epitope prediction.
- ELISAeq: Computer program for determining the concentration of antibody/antigen from ELISA data.
- IgPred: Prediction of antibody specific B-cell epitope.
- LBtope: A server for predicting linear B-cell epitopes.
- mhc: Matrix Optimization Technique for Predicting MHC binding Core.
- mhcbench: Evaluation of MHC Binding Peptide Prediction Algorithms.
- mhc2pred:SVM based method for prediction of promiscuous MHC class II binders.
- MHCBN: A database od Major Histocompatibility Complex (MHC) Binding,Non-binding peptides.
- MHCBN4: A database of MHC/TAP binding peptides and T-cell epitopes.
- MtbVeb: A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
- MycoTb: A software for managing mycobacterium tuberculosis.
- Pcleavage: Identification of protesosomal cleavage sites in a protein sequence.
- PolysacDB: A comprehensive Database of microbial Polysaccharide antigens and their antibodies.
- ProPred: A webserver to predict MHC Class-II binding regions in an antigen sequence.
- ProPred-1: Prediction of promiscuous MHC Class-I binders.
- TAPPred: A webserver for predicting binding affinity of peptides toward the TAP transporter.
- 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.
- AntiInflam: Prediction of anti-inflammatory proteins/peptides: an insilico approach.
- BCPRED: A novel method for predicting linear B-cell epitopes using the subsequence kernel.
- BepiPred: BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures.
- 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.
- CEP: a conformational epitope prediction server.
- dbDiarrhea: the database of pathogen proteins and vaccine antigens from diarrheal pathogens.
- 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
- ElliPro: Used for prediction and analysis of antibody epitopes in a protein structure.
- EpiJen: It is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes.
- EpiPred: Method to identify the epitope region on the antigen, given the structures of the antibody and the antigen.
- Epitopia: Web-based tool that aims to predict immunogenic regions in either a protein three-dimensional structure or a linear sequence.
- EPMeta: novel server applications for discontinuous epitope prediction.
- EPSVR: novel server applications for discontinuous epitope prediction.
- HLaffy: Estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials.
- IEDB analysis: This site provides a collection of tools for the prediction and analysis of immune epitopes.
- MAPPP : Prediction of potential antigenic epitopes presented on the cell surface by MHC I molecules to CD8 positive T lymphocytes.
- MHCPred: A server for quantitative prediction of peptide–MHC binding.
- MULTIPRED2: It is used to screen peptide that binds to multiple alleles belonging to HLA class I and class II DR super types.
- NetChop: Produces neural network predictions for cleavage sites of the human proteasome.
- NetCTL: Web-based tool designed for predicting human CTL epitopes in any given protein.
- NetMHC: NetMHC-4.0 is used for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment.
- NetMHCPan: MHC Class I interaction predictions integrating eluted ligand and peptide binding affinity data
- 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.
- NetMHCIIPan: NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules.
- PAProC: Prediction algorithm for proteasomal cleavages. Also linked to diseases like Alzheimer's , Parkinson's and Huntington's disease.
- PEASE (Predicting Epitopes using Antibody Sequence): Predicts antibody-specific epitopes using sequence information of the antibody.
- ProInflam: A webserver for the prediction of proinflammatory antigenicity of peptides and proteins.
- RANKPEP: Used for both class I and II MHC, based on the comparison of sequence similarities, using position-specific scoring matrices method.
- 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).
- SYFPEITHI: It is a database for MHC ligands and peptide motifs.