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MHC class II binding detection software tools | Immunoinformatics

CD4+ T-cell epitopes play a crucial role in eliciting vigorous protective immune responses during peptide (epitope)-based vaccination. The prediction of these epitopes focuses on the peptide binding process by MHC class II proteins. The ability to…
MHCPred
Web

MHCPred

Uses the additive method to predict the binding affinity of major…

Uses the additive method to predict the binding affinity of major histocompatibility complex (MHC) class I and II molecules and the Transporter associated with Processing (TAP). MHCPred is an online…

FRED
Desktop

FRED FRamework for Epitope Detection

A versatile immunoinformatics software framework enabling a unified interface…

A versatile immunoinformatics software framework enabling a unified interface to many tools, from epitope prediction, HLA typing, to epitope selection and assembly. Its openness and easy…

ProPred
Web

ProPred

Analyses sequence data to predict MHC class II binding regions in antigenic…

Analyses sequence data to predict MHC class II binding regions in antigenic protein sequences. Propred (generates text or graphic outputs, presents the binding score calculated from matrix in tabular…

EpiToolKit
Web

EpiToolKit

A virtual workbench for immunological questions with a focus on vaccine design.…

A virtual workbench for immunological questions with a focus on vaccine design. EpiToolKit offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction,…

SVMHC
Web

SVMHC

A server for prediction of both MHC class I and class II binding peptides.…

A server for prediction of both MHC class I and class II binding peptides. SVMHC offers fast analysis of a wide range of alleles and prediction results are given in several comprehensive formats. The…

TepiTool
Desktop
Web

TepiTool

A pipeline for computational prediction of t cell epitope candidates. TepiTool,…

A pipeline for computational prediction of t cell epitope candidates. TepiTool, which is part of the Immune Epitope Database (IEDB), provides some of the top MHC binding prediction algorithms for…

Epitopemap
Desktop
Web

Epitopemap

A self-contained web application for calculating and viewing epitope…

A self-contained web application for calculating and viewing epitope predictions. Epitopemap allows integration of multiple epitope prediction methods for any number of proteins in a genome. The tool…

TEpredict
Desktop

TEpredict predicting T-cell epitopes

Allows T-cell epitope prediction. TEpredict allows prediction of (i) peptides…

Allows T-cell epitope prediction. TEpredict allows prediction of (i) peptides binding to various allelic variants of class I and II Major Histocompatibility Complex (MHC) molecules, (ii) proteasomal…

NNAlign
Desktop
Web

NNAlign

Allows prediction of peptide– major histocompatibility complex (MHC) class II…

Allows prediction of peptide– major histocompatibility complex (MHC) class II binding affinity. NNAlign is a motif discovery method based on artificial neural networks (ANNs). The web server allows…

G T A T C G C T A
LIGAP
Desktop

LIGAP

Allows integrative analysis and visualization of multiple lineages over whole…

Allows integrative analysis and visualization of multiple lineages over whole time-course profiles. LIGAP is a computational methodology that is widely applicable to quantify differential time-course…

EpiTOP
Web

EpiTOP

A server predicting MHC class II binding based on proteochemometrics. EpiTOP is…

A server predicting MHC class II binding based on proteochemometrics. EpiTOP is a QSAR approach for ligands binding to several related proteins. It uses a quantitative matrix to predict binding to 12…

HLA-DR4Pred
Desktop
Web

HLA-DR4Pred

An SVM and ANN based HLA-DRB1*0401 (MHC class II alleles) binding peptides…

An SVM and ANN based HLA-DRB1*0401 (MHC class II alleles) binding peptides prediction method. The accuracy of the SVM and ANN based methods is ~86% and ~78% respectively. The performance of the…

EpiDOCK
Web

EpiDOCK

Provides access to a collection of accurate major histocompatibility complex…

Provides access to a collection of accurate major histocompatibility complex (MHC) class II binding prediction models, which were derived via molecular docking. EpiDOCK is structure-based and…

CTLPred
Desktop
Web

CTLPred

A direct method for prediction of CTL epitopes crucial in subunit vaccine…

A direct method for prediction of CTL epitopes crucial in subunit vaccine design. In direct methods the information or patterns of T cell epitopes instead of MHC binders were used for the development…

TEPITOPEpan
Desktop
Web

TEPITOPEpan

Extends the original TEPITOPE method to peptide binding prediction to more…

Extends the original TEPITOPE method to peptide binding prediction to more alleles. Generally speaking, TEPITOPEpan can make the qualitative peptide binding prediction to any HLA-DR molecule of known…

GPS-MBA
Web

GPS-MBA

A software package was developed for the prediction of I-A(g7) and HLA-DQ8…

A software package was developed for the prediction of I-A(g7) and HLA-DQ8 epitopes. Using experimentally identified epitopes as the training data sets, a previously developed GPS (Group-based…

EpicCapo
Desktop

EpicCapo

Identifies candidates of promiscuous epitopes and positions of nonapeptides in…

Identifies candidates of promiscuous epitopes and positions of nonapeptides in peptide-MHC (pMHC) binding. Peptides were encoded numerically by combining information on the pMHC contact sites with…

POPISK
Web

POPISK

A computational method based on support vector machines with a weighted string…

A computational method based on support vector machines with a weighted string kernel to predict peptide immunogenicity and identify important recognition positions. POPISK yields a mean 10-fold…

PREDIVAC
Web

PREDIVAC

A method to predict HLA class II peptide binding, based on the…

A method to predict HLA class II peptide binding, based on the specificity-determining residue (SDR) concept, which covers 95% of MHC class II allelic variants (DR locus). It is implemented as a…

SMM-align
Web

SMM-align

A stabilization matrix alignment method that allows for direct prediction of…

A stabilization matrix alignment method that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark…

SVRMHC
Web

SVRMHC

An accurate and easy-to-use prediction server for epitope-MHC binding with…

An accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. SVRMHC is a valuable resource for T cell epitope researchers.

EpiJen
Web

EpiJen

A reliable multi-step algorithm for T cell epitope prediction, which belongs to…

A reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent…

ARB
Web

ARB Average Relative Binding

Predicts IC(50) values allowing combination of searches involving different…

Predicts IC(50) values allowing combination of searches involving different peptide sizes and alleles into a single global prediction. A computer program was developed to automate the generation and…

NetMHCIIpan
Web

NetMHCIIpan

A pan-specific method capable of predicting peptide binding to any HLA class II…

A pan-specific method capable of predicting peptide binding to any HLA class II molecule with a defined protein sequence. The method employs a strategy common for HLA-DR, HLA-DP and HLA-DQ molecules…

HLArestrictor
Web

HLArestrictor

A tool for patient-specific predictions of HLA restriction elements and optimal…

A tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides. Given the high-resolution (i.e. 4-digit) HLA typing of the individual, HLArestrictor predicts…

MHCcluster
Web

MHCcluster

A tool to functionally cluster MHC molecules based on their predicted binding…

A tool to functionally cluster MHC molecules based on their predicted binding specificity. MHCcluster provides highly intuitive heat-map and graphical tree-based visualizations of the functional…

PAAQD
Desktop

PAAQD

A method for T-cell reactivity prediction. Nonapeptides were encoded…

A method for T-cell reactivity prediction. Nonapeptides were encoded numerically, using combining information of amino acid pairwise contact potentials (AAPPs) and quantum topological molecular…

MULTIPRED
Web

MULTIPRED

A computational system for facile prediction of peptide binding to multiple…

A computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide…

MHCMIR
Desktop
Web

MHCMIR

A server for predicting the binding affinity of MHC-II peptides using multiple…

A server for predicting the binding affinity of MHC-II peptides using multiple instance regression. The current version supports 13 HLA-DR alleles and three mouse H2-IA alleles. The submission form,…

HLAPred
Web

HLAPred

The method can identify and predict HLA binding regions from antigen sequence.…

The method can identify and predict HLA binding regions from antigen sequence. The method allows identification and prediction for 87 alleles, out of which 51 belong to Class I and 36 belongs to…

MMBPred
Web

MMBPred

The identification of peptides in an antigenic sequence that can bind with high…

The identification of peptides in an antigenic sequence that can bind with high affinity to a wide range of MHC alleles is one of the challenges in subunit vaccine design. The mutation of natural…

FDR4
Web

FDR4

This server is meant for the prediction of binding affinity of peptide binders…

This server is meant for the prediction of binding affinity of peptide binders in an antigenic sequence for a MHC class II allele HLA-DRB1*0401. Methods developed in the past can only predict whether…

MHC
Web

MHC

Matrix Optimization Technique for identification of binding core in MHC II…

Matrix Optimization Technique for identification of binding core in MHC II binding peptides. The prediction method used in this server is based on MOT and relies on the thought that binders have…

MHC2Pred
Web

MHC2Pred

The helper T cell epitopes are subset of MHC class II ligands and play a…

The helper T cell epitopes are subset of MHC class II ligands and play a decisive role in initiation and maintenance of immune response. MHC2Pred is a support vector machine (SVM)-based method for…

MHCBench
Web

MHCBench

An interface developed for evaluating the Major Histocompatibility Complex…

An interface developed for evaluating the Major Histocompatibility Complex (MHC) binding peptide prediction algorithms. MHCBench allows the users to compare the performance of the old/new prediction…

MultiRTA
Web

MultiRTA

Predicts peptide binding affinities for major histocompatibility complex (MHC)…

Predicts peptide binding affinities for major histocompatibility complex (MHC) allotypes not included in the training set. MultiRTA is a generalization of the RTA method that accounts for…

BiodMHC
Web

BiodMHC

Gathers several prediction models. BiodMHC provides researchers an online…

Gathers several prediction models. BiodMHC provides researchers an online interface that allowing them to obtain binding information simultaneously using a variety of methods. This platform offers…

MHC-BPS
Web

MHC-BPS

A web-based MHC-binder prediction server that uses support vector machines for…

A web-based MHC-binder prediction server that uses support vector machines for predicting peptide binders of flexible lengths for 18 MHC class I and 12 class II alleles from sequence-derived…

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