MHC-I Download

Scoring matrices of SMM and SMMPMBEC - Download

To download the dataset in tar.gz format:

Dataset used for retraining the IEDB class I binding prediction tools.

Description of the dataset: The dataset is largely identical to that of Kim et al (2014), described above, but includes additional data that was not publicly available at the time.
Date of the dataset generation: 2013
Details on the dataset generation: The dataset was compiled from three sources: the IEDB, the Sette lab, and the Buus lab. If a peptide/allele combination had more than 1 measurement among the three sources, its geometric mean was taken.
Data format: Compressed text file containing binding data.
Dataset availability: binding_data_2013.zip

Dataset used for training and testing of the NetMHCpan-4.1 method

Dataset availability: https://services.healthtech.dtu.dk/suppl/immunology/NAR_NetMHCpan_NetMHCIIpan/

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

Description of the dataset: The training binding data are partitioned in 5 files to be used for cross-validation. For instance do the f000_ba and f000_el files contain the binding affinity and eluted ligand training data, and the c000_ba and c000_el files the binding affinity and eluted ligand test data for the first cross-validation partitioning. It is critical that this data partitioning is maintained.
Note that the BA data - binding affinity - are identical to the ones used for training of NetMHC-4.0 and NetMHCpan-3.0.
Dataset availability: https://services.healthtech.dtu.dk/immunology/NetMHCpan-4.0/

MHC-I binding predictions - Download

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

ann
smm
smmpmbec
comblib_sidney2008
consensus
netmhcpan
pickpocket
netmhccons

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To download the tools in tar.gz format:
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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