MHC Class II, IEDB, Jensen et al.

Dataset Description

Major histocompatibility complex class II (MHC‐II) molecules are found on the surface of antigen‐presenting cells where they present peptides derived from extracellular proteins to T helper cells. Useful to identify T‐cell epitopes. An organized datasets by NetMHCIIpan for MHC class II collected from IEDB 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='MHC2_IEDB_Jensen')

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

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

References

• [1] Jensen, Kamilla Kjaergaard, et al. “Improved methods for predicting peptide binding affinity to MHC class II molecules.” Immunology 154.3 (2018): 394-406.
• [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.