ibm/biomed.omics.bl.sm.ma-ted-458m.tcr_epitope_bind

T-cell receptor (TCR) binding to immunogenic peptides (epitopes) presented by major histocompatibility complex (MHC) molecules is a critical mechanism in the adaptive immune system, essential for antigen recognition and triggering immune responses. The T-cell receptor (TCR) repertoire exhibits considerable diversity, consisting of an α-chain and a β-chain that function together to enable T cells to recognize a wide array of epitopes. The β-chain is especially significant, as it is crucial for the early stages of T-cell development and possesses greater variability, which enhances the TCR’s capacity to identify diverse pathogens effectively. However, understanding the specific interactions between TCRs and epitopes remains a significant challenge due to the vast variability in TCR sequences. Accurate prediction of TCR-peptide binding from sequence data could revolutionize immunology by offering deeper insights into a patient’s immune status and disease history. This capability holds potential applications in personalized immunotherapy, early diagnosis, and the treatment of diseases such as cancer and autoimmune disorders. In silico tools designed to model TCR-peptide interactions could also facilitate the study of therapeutic T-cell efficacy and assess cross-reactivity risks, presenting a transformative opportunity for precision medicine.

The benchmark defined in: https://academic.oup.com/bioinformatics/article/37/Supplement_1/i237/6319659?login=false Data retrieved from: https://tdcommons.ai/multi_pred_tasks/tcrepitope

Model Summary

• Developers: IBM Research
• GitHub Repository: https://github.com/BiomedSciAI/biomed-multi-alignment
• Paper: https://arxiv.org/abs/2410.22367
• Release Date: Oct 28th, 2024
• License: Apache 2.0.

Usage

Using ibm/biomed.omics.bl.sm.ma-ted-458m.tcr_epitope_bind requires installing https://github.com/BiomedSciAI/biomed-multi-alignment

pip install git+https://github.com/BiomedSciAI/biomed-multi-alignment.git

A simple example for a task already supported by ibm/biomed.omics.bl.sm.ma-ted-458m.tcr_epitope_bind:

from mammal.examples.tcr_epitope_binding.main_infer import load_model, task_infer

tcr_beta_seq = "NAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSWDRVLEQYFGPGTRLTVT"
epitope_seq = "LLQTGIHVRVSQPSL"

model_inst, tokenizer_op = load_model(device="cpu")
result = task_infer(
    model=model_inst,
    tokenizer_op=tokenizer_op,
    tcr_beta_seq=tcr_beta_seq,
    epitope_seq=epitope_seq,
)
print(f"The prediction for {epitope_seq} and {tcr_beta_seq} is {result}")

See our detailed example at: on https://github.com/BiomedSciAI/biomed-multi-alignment

Citation

If you found our work useful, please consider giving a star to the repo and cite our paper:

@misc{shoshan2024mammalmolecularaligned,
      title={MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language}, 
      author={Yoel Shoshan and Moshiko Raboh and Michal Ozery-Flato and Vadim Ratner and Alex Golts and Jeffrey K. Weber and Ella Barkan and Simona Rabinovici-Cohen and Sagi Polaczek and Ido Amos and Ben Shapira and Liam Hazan and Matan Ninio and Sivan Ravid and Michael M. Danziger and Joseph A. Morrone and Parthasarathy Suryanarayanan and Michal Rosen-Zvi and Efrat Hexter},
      year={2024},
      eprint={2410.22367},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM},
      url={https://arxiv.org/abs/2410.22367}, 
}