ronig/protein_biencoder

Peptriever: A Bi-Encoder for large-scale protein-peptide binding search

For training details see our Application Note.

Training code can be found in our Github repo.

A live demo is available on our application page

Usage

import torch
from transformers import AutoModel, AutoTokenizer

tokenizer = AutoTokenizer.from_pretrained("ronig/protein_biencoder")
model = AutoModel.from_pretrained("ronig/protein_biencoder", trust_remote_code=True)
model.eval()

peptide_sequence = "AAA"
protein_sequence = "MMM"
encoded_peptide = tokenizer.encode_plus(peptide_sequence, return_tensors='pt')
encoded_protein = tokenizer.encode_plus(protein_sequence, return_tensors='pt')

with torch.no_grad():
    peptide_output = model.forward1(encoded_peptide)
    protein_output = model.forward2(encoded_protein)

print("distance: ", torch.norm(peptide_output - protein_output, p=2))

Version

Model checkpint: peptriever_2023-06-23T16:07:24.508460