MHC class I binding and epitope prediction based on modeled physicochemical properties of peptides
MHC class I binding and epitope prediction based on modeled physicochemical properties of peptides.
MHCLovac is a result of my personal interests and some free time. It is not a result of thorough scientific research. That said, MHCLovac is not too bad in terms of predictions it makes and I plan to improve it further if possible.
- version 3.0
- epitope prediction.
- ic50 predictions are replaced with binding score. The higher the score the stronger the binding.
- single prediction algorithm replaced with collection of algorithms, prediction consensus.
MHCLovac is a command line tool used for MHC Class I binding and epitope prediction. It uses modeled physicochemical properites of target peptides to predict binding and epitope scores. The modeling is accomplished using proteinko python package (also my work). MHCLovac is not constrained by the length of target peptide sequence and is capable of making predictions for peptides of any length. Prediction is carried out by a collection of regression and classification algorithms. Algos are trained on data obtained from two sources: dataset used for retraining the IEDB class I binding prediction tools http://tools.iedb.org/static/main/binding_data_2013.zip and IEDB database (www.iedb.org).
Training results and a list of supported MHC alleles is available in training/results folder.
Trained models are benchmarked using ROC-AUC method. Benchmarking method is explained in benchmark folder.
pip install mhclovac
mhclovac -f example.fasta -m HLA-B*44:02 -l 11
sequence mhc peptide_length sequence_name binding_score epitope_score combined_score MEIFIEVFSHF HLA-B*44:02 11 MEIFIEVFSHF HLA-B44:02 0.523205 0.965484 1.488688 EIFIEVFSHFL HLA-B*44:02 11 MEIFIEVFSHF HLA-B44:02 0.087188 0.512132 0.599320 IFIEVFSHFLL HLA-B*44:02 11 MEIFIEVFSHF HLA-B44:02 0.039142 0.159362 0.198503 FIEVFSHFLLQ HLA-B*44:02 11 MEIFIEVFSHF HLA-B44:02 0.114877 0.264553 0.379430 IEVFSHFLLQL HLA-B*44:02 11 MEIFIEVFSHF HLA-B44:02 0.317922 0.964168 1.282090
sequence_name- Fasta sequence name or name provided by
mhc- MHC allele
binding_score- Higher score means better binding
epitope_score- Higher score means a better epitope
combined_score- Sum of binding and epitope scores if both are available
Donate to support my work
This work is done on my own budget so if you like you can support me by donating Bitcoin. Any amount donated will be appreciated. Thank you!
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