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MHC class I binding detection software tools | Immunoinformatics

A key role in cell-mediated immunity is dedicated to the major histocompatibility complex (MHC) molecules that bind peptides for presentation on the cell surface. Several in silico methods capable of predicting peptide binding to MHC class I have…
NetMHC
Web
Desktop

NetMHC

Predicts peptide-major histocompatibility complex (MHC) class I binding…

Predicts peptide-major histocompatibility complex (MHC) class I binding affinity. NetMHC is based on artificial neural networks that allows insertions and deletions in the alignment. It is able to…

NetMHCpan
Web

NetMHCpan

Allows prediction of peptide binding affinity. NetMHCpan is a simple…

Allows prediction of peptide binding affinity. NetMHCpan is a simple pan-specific machine learning method. It improves predictive performance by characterizing the binding specificity of a given…

PickPocket
Web
Desktop

PickPocket

Extrapolates from variants with known binding specificity to those where no…

Extrapolates from variants with known binding specificity to those where no experimental data are available. PickPocket uses information derived from similar protein structures to infer which…

NetMHCstab
Web

NetMHCstab

Allows prediction of stability of peptide–major histocompatibility complex…

Allows prediction of stability of peptide–major histocompatibility complex class I (MHC-I) complexes. NetMHCstab is a web-server that uses artificial neural networks (ANNs). The software was…

POPI
Web

POPI Prediction Of Peptide Immunogenicity

Predicts peptide immunogenicity. POPI allows users to mine a feature set of…

Predicts peptide immunogenicity. POPI allows users to mine a feature set of informative physicochemical properties from major histocompatibility complex (MHC) class I binding peptides. It is based on…

MixMHCpred
Desktop

MixMHCpred

Intends to score different peptides and prioritize the most likely human…

Intends to score different peptides and prioritize the most likely human leukocyte antigen-I (HLA-I) ligands. MixMHCpred is a scalable framework and a predictor of HLA-I ligands displayed at the cell…

DynaPred
Algorithm

DynaPred

Allows at the same time a fast prediction of major histocompatibility complex…

Allows at the same time a fast prediction of major histocompatibility complex (MHC) class I binders and an efficient construction of docked peptide conformations. DynaPred is a combined two-step…

NetMHCstabpan
Web

NetMHCstabpan

Predicts peptide–major histocompatibility complex (MHC)-I complex stability.…

Predicts peptide–major histocompatibility complex (MHC)-I complex stability. NetMHCstabpan is based on neural network pan-specific method. It allows the user to include affinity predictions. The…

NetMHCcons
Web

NetMHCcons

Predicts binding of peptides to any known major histocompatibility complex…

Predicts binding of peptides to any known major histocompatibility complex (MHC) class I molecule. NetMHCcons is a server that allows the user in an automatic manner to obtain the most accurate…

HLaffy
Web

HLaffy

A novel and efficient epitope prediction method that predicts epitopes for any…

A novel and efficient epitope prediction method that predicts epitopes for any Class-1 HLA allele, by estimating the binding strengths of peptide-HLA complexes which is achieved through learning…

WAPP
Web

WAPP Whole Antigen Processing Prediction

Predicts events in the processing pathway of major histocompatibility complex…

Predicts events in the processing pathway of major histocompatibility complex (MHC) class I antigens. WAPP is a combined model that allows users to detect three major events included in this…

GradDock
Desktop

GradDock

Decouples global and local conformational searches and generates diverse…

Decouples global and local conformational searches and generates diverse native-like peptide conformations for peptide binding to major histocompatibility complex class I (pMHC-I). GradDock uses a…

MHCflurry
Desktop

MHCflurry

Predicts peptide-major histocompatibility complex class-I (pMHC-I) binding…

Predicts peptide-major histocompatibility complex class-I (pMHC-I) binding affinities. MHCflurry contains (1) an embedding layer which transforms amino acids to learned vector representations, (2) a…

MHCnuggets
Desktop

MHCnuggets

Predicts peptide binding to Major Histocompatibility Complex (MHC) Class I…

Predicts peptide binding to Major Histocompatibility Complex (MHC) Class I proteins. MHCnuggets is based on deep recurrent neural networks. It augments the training data artificially or train…

HLA-Vec
Desktop

HLA-Vec

Maps amino acids to a 15- dimensional vector space. HLA-Vec is a distributed…

Maps amino acids to a 15- dimensional vector space. HLA-Vec is a distributed representation of amino acids that can be used for a variety of downstream proteomic machine learning tasks. This…

HLA-CNN
Desktop

HLA-CNN Human Leukocyte Antigen-Convolutional Neural Network

Extracts a vector space distributed representation of amino acids from Human…

Extracts a vector space distributed representation of amino acids from Human Leukocyte Antigen (HLA) peptide data that preserved property critical for covalent bonding. HLA-CNN is a deep…

Expitope
Web

Expitope

In order to see potential off-target recognition when designing new lead…

In order to see potential off-target recognition when designing new lead targets, until now one needed to search protein databases for approximate hits and than evaluate each hit for its potential to…

Episopt
Web

Episopt

Allows selection of epitope combinations providing the largest population…

Allows selection of epitope combinations providing the largest population protection coverage (PPC). Episopt predicts epitope human leukocyte antigen (HLA) I binding profiles and identifies minimal…

MetaMHCpan
Web

MetaMHCpan

Allows major histocompatibility complex (MHC) peptide binding prediction.…

Allows major histocompatibility complex (MHC) peptide binding prediction. MetaMHCpan predicts peptide binders of a variety of MHC alleles (through MetaMHCIpan and MetaMHCIIpan). This tool uses…

ProPred1
Desktop
Web

ProPred1

An on-line service for identifying the MHC Class-I binding regions in antigens.…

An on-line service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles, proteasomal and immunoproteasomal models. The main aim of ProPred1…

NetTepi
Web

NetTepi

Predicts T-cell epitopes from protein sequences. The method integrates three…

Predicts T-cell epitopes from protein sequences. The method integrates three prediction types, peptide-MHC binding affinity, peptide-MHC stability and T-cell propensity.

HLA Assignment
Web
Desktop

HLA Assignment

Provides a statistical model for identifying Human Leukocyte Antigen…

Provides a statistical model for identifying Human Leukocyte Antigen (HLA)-restricted epitopes from ELISpot data. By looking at patterns across a broad range of donors, HLA Assignment can determine…

NetCTL
Web

NetCTL

Predicts CTL epitopes in protein sequences. The method integrates prediction of…

Predicts CTL epitopes in protein sequences. The method integrates prediction of peptide MHC class I binding, proteasomal C terminal cleavage and TAP transport efficiency. The server allows for…

NetCTLpan
Web

NetCTLpan

A pan-specific major histocompatibility complex (MHC) class I epitope…

A pan-specific major histocompatibility complex (MHC) class I epitope predictor. The method integrates predictions of proteasomal cleavage, transporter associated with antigen processing (TAP)…

RANKPEP
Web

RANKPEP

Ranks all possible peptides from an input protein using the PSSM coefficients.…

Ranks all possible peptides from an input protein using the PSSM coefficients. The predictive power of the method was evaluated by running RANKPEP on proteins known to bear MHCI K(b)- and…

Epitope…
Web
Desktop

Epitope Prediction

Predicts HLA (Human Leukocyte Antigen) class I restricted cytotoxic T…

Predicts HLA (Human Leukocyte Antigen) class I restricted cytotoxic T lymphocytes (CTL) epitopes. Epitope Prediction which is based on logistic regression, is simple to implement. It is solved by…

MHCLIG
Web

MHCLIG

Predicts the ligand-type specificity of major histocompatibility complex class…

Predicts the ligand-type specificity of major histocompatibility complex class I (MHC I) proteins. MHCLIG enables the prediction of three-known ligand-type specificities of MHC I proteins (P:…

nHLAPred
Web

nHLAPred

An accurate MHC binders prediction method for the large number of class I MHC…

An accurate MHC binders prediction method for the large number of class I MHC alleles. nHLAPred allows to identify the promiscuous MHC class I binders (peptides that can bind to large number of…

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