The ability to predict B cell epitopes from antigen sequences is critical for biomedical research and many clinical applications. However, despite substantial efforts over the past 20 years, the performance of even the best B cell epitope prediction software is still modest. Based on the idea of T-B reciprocity, BepiTBR is a B cell epitope prediction model that demonstrates improved performance by incorporating prediction of nearby CD4+ T cell epitopes close to the B cell epitopes.

Epitope Mode analyzes specific epitopes within proteins. This mode requires epitope sequences and their corresponding full antigen protein sequences


Example command using provided example files:

(replace paths with appropriate paths according to user's particular installation)

raku BepiTBR.raku \
--motif0_file=examples/test_data_BepiTBR/Ind-positive.txt \
--full0_file=examples/test_data_BepiTBR/peptide_with_full_length.txt \
--bepipred2=bp2/bin/activate \
--bepipred1=/home/exampleUser/bp1/bepipred-1.0/bepipred \
--LBEEP=/home/exampleUser/LBEEP/ \
--MixMHC2pred=/home/exampleUser/MixMHC2pred/MixMHC2pred_unix \
--netMHCIIpan=/home/exampleUser/netMHCIIpan-3.2/netMHCIIpan \
--dir=/home/exampleUser/BepiTBR/examples/test_output_BepiTBR \


Name Explanation
motif0_file candidate epitopes file
full0_file full protein sequences file
bepipred2 the conda environment activation file for BepiPred 2.0
bepipred1 path to the BepiPred 1.0 executable
LBEEP path to the LBEEP directory
MixMHC2pred path to the MixMHC2pred executable
netMHCIIpan path to the NetMHCIIpan 3.2 executable
dir output directory
thread number of CPU thread to use; system dependent


1. Required tools (BepiPred 1.0, BepiPred 2.0, LBEEP 1.0, NetMHCIIpan 3.2, MixMHC2pred) must be installed before executing model. For more details about installation and other dependencies, please visit our GitHub.

2. For BepiPred 2.0, this tool requires an isolated python virtual environment (python 2.7). After installation, It is recommended to move the bp2 env directory into the BepiTBR main directory.