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
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.
By downloading the standalone tool, you are consenting to be bound by and become a party as the "Licensee" for the use of NetMHC 3.0".
Also you are consenting the terms and conditions of the Non-Profit Open Software License ("Non-Profit OSL") version 3.0
Please read folowing two agreements before proceeding. If you do not agree to all of the terms of these two agreements, you must not click the download button, not install the product nor use the product, and you do not become a LICENSEE under these agreements.
To download the tools in tar.gz format:
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IEDB Tools Downloads
Complete Download: IEDB Analysis Resource Virtual Machine ImageFor 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 DownloadsMany 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.
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.
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.
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.
Epitope Cluster Analysis
This tool groups epitopes into clusters based on sequence identity. A cluster is defined as a group of sequences which have a sequence similarity greater than the minimum sequence identity threshold specified.
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.
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.