MHC Class I, IEDB-IMGT, Nielsen et al.

Dataset Description

Binding of peptides to MHC class I molecules (MHC-I) is essential for antigen presentation to cytotoxic T-cells. An organized datasets by NetMHCpan for MHC class I collected from IEDB and IMGT/HLA database.

Task Description

Regression. Given the amino acid sequence of peptide and the pseudo amino acid sequence of MHC, predict the binding affinity.

Usage Example

from tdc_ml.multi_pred import PeptideMHC

data = PeptideMHC(name='MHC1_IEDB-IMGT_Nielsen')

# Access the data
df = data.get_data()
print(df.head())

# Get train/val/test splits
split = data.get_split()
print(split)

References

• [1] Nielsen, Morten, and Massimo Andreatta. “NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets.” Genome medicine 8.1 (2016): 1-9.
• [2] Vita, Randi, et al. “The immune epitope database (IEDB): 2018 update.” Nucleic acids research 47.D1 (2019): D339-D343.
• [3] Zeng, Haoyang, and David K. Gifford. “Quantification of uncertainty in peptide-MHC binding prediction improves high-affinity peptide Selection for therapeutic design.” Cell systems 9.2 (2019): 159-166.