MHC-II Download

MHC-II binding dataset - Download

This MHC class II binding affinity dataset consists of 44, 541 experimentally measured binging affinities covering 26 alleric variants.
Two sets of randomly splitted 5-fold cross validation data are provided: the entire dataset ("ALL") and the similarity reduced dataset ("SR").

To download the dataset in tar.gz format:

Prediction scores for MHC-II binding dataset - Download

The prediction scores for the six implemented algorithms based on above dataset can be download here. The scores were generate via 5-fold cross validation based on two sets of data: the entire dataset ("ALL") and the similarity reduced dataset "SR".

To download the scores in tar.gz format:

Combinatorial peptide scanning library scoring matrices - Download

This file contains the scoring matrices for sixteen MHC class II alleles developed from the combinatorial peptide scanning library data.

To download the dataset in tar.gz format:

Dataset used for training and testing of the NetMHCIIpan-4.0 method

Dataset availability: http://www.cbs.dtu.dk/suppl/immunology/NAR_NetMHCpan_NetMHCIIpan/

Dataset used for training and testing of the NetMHCIIpan-3.2 method

Dataset availability: http://www.cbs.dtu.dk/suppl/immunology/NetMHCIIpan-3.2/

MHC-II binding predictions - Download

The MHC_II binding tool contains a collection of following peptide binding prediction methods for Major Histocompatibility Complex (MHC) class II molecules.The collection is a mixture of pythons scripts and linux 32-bit environment specific binaries.

combinatorial library
smm_align
tepitope
Consensus
NetMHCIIpan

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IEDB Tools Downloads

Complete Download: IEDB Analysis Resource Virtual Machine Image

For users that would like to run the entire analysis resource locally, a virtual machine image file is available with a paid commercial license. The image is kept in sync with the current version of the IEDB Analysis Resource and is updated on a six month cycle. Please contact us for details on licensing options.

Standalone Downloads

Many of the tools hosted on the IEDB-AR are available as command-line tools. They are freely available to academic users through an open source license. Please contact us to inquire about a commercial license or if you have any questions in general. For a complete list of standalone tools, including previous versions, please click here.

Linear B cell epitope predictor
This allows for scoring of amino acid residues using the 6 scale-based methods of the linear B cell epitope prediction tool.

Linear B cell epitope predictor

MHC class I & II epitope predictors
For users with batch processing needs, the MHC class I and II binding prediction tools are available as standalone scripts for download. These command line tools are kept in sync with the web tools and should therefore produce the same results as clicking through the web interface.

ElliPro
This will produce the same output as the web version of the tool but does not include the initial template finding functionality. It accepts either a PDB ID or a path to a PDB file as input. Usage instructions are printed by calling the program without any parameters.

ElliPro

Class I Immunogenicity
This tool uses amino acid properties as well as their position within the peptide to predict the immunogenicity of a peptide MHC (pMHC) complex.

Class I Immunogenicity

Proteasomal Cleavage Prediction
The distributions 'IEDB_NetChop-1.0.tar.gz' contains methods for NetChop, NetCTL and NetCTLpan.
NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL is a predictor of T cell epitopes along a protein sequence. It also employs a neural network architecture. NetCTLpan is an update to the original NetCTL server that allows for prediction of CTL epitope with restriction to any MHC molecules of known protein sequence.

Proteasomal Cleavage Prediction

Population Coverage
This tool calculates the fraction of individuals predicted to respond to a given epitope set on the basis of HLA genotypic frequencies and on the basis of MHC binding and/or T cell restriction data. HLA allele genotypic frequencies were obtained from Allele Frequency database.

Population Coverage

TCRMatch
TCRMatch compares input CDR3b sequences against curated CDR3b sequences in the IEDB to find matches that are predicted to share epitope specificity. Matches are determined by sequence similarity, which is scored using a comprehensive k-mer comparison.

TCRMatch