BepiPred-2.0: Sequential B-Cell Epitope Predictor

Here, one can download the data used for training, testing and evaluating this method.

IEDB Linear Epitopes

File Format: Fasta
Header: <Positive/Negative>ID_<IEDB_Epitope_ID>
The header explains whether the sequence has a negative or positive epitope sequence mapped onto it.

Epitope: Uppercased
Non-Epitope: Lowercased

Download: IEDB Linear Epitope Dataset

PDB Structural Epitopes

File Format: Fasta
Header: <PDBID>_<Heavy_Chain_ID><Light_Chain_ID> <Antigen_Chain_ID> <Partition>
The header explains which antibody chains and antigen chains in a given PDB have been used. The partition is which of the 5 randomly split partitions it belonged to and the partition EVAL is the completely left out PDBs.

Epitope: Uppercased
Non-Epitope: Lowercased

Download: PDB Combined Epitopes Dataset


Portable Version

Would you prefer to run BepiPred at your own site? BepiPred 2.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at software@cbs.dtu.dk.

Previous Versions

For previous version go to: BepiPred-1.0

Getting Help

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