ResPepBind
A 10-fold residual neural network ensemble for peptide-protein interaction prediction.
The official checkpoint ZIP is hosted separately as a GitHub Release. The first prediction automatically downloads all 10 fold checkpoints into ~/.cache/respepbind/models/. It also downloads the pretrained ProtT5 encoder from Hugging Face when missing residue embeddings are first generated.
Predict: input FASTA or CSV (CPU or GPU)
Install package with pip install respepbind from PyPI published distribution.
FASTA:
>positive_1
Peptide: MLGP
Protein: MAEVPPGPSSLLPPPAPPAPAAVE
>negative_1
Peptide: ACDW
Protein: MLEVKQRL
CSV:
id,peptide,protein,true_label
pair1,MLGP,MAEVPPGPSSLLPPPAPPAPAAVE,1
pair2,ACDW,MLEVKQRL,
Run:
respepbind --fasta examples/pairs.fasta --device cpu --output-csv results/fasta.csv
respepbind --csv examples/pairs.csv --device cuda:0 --output-csv results/csv_gpu.csv
Or use wrappers:
./scripts/predict_cpu.sh --fasta examples/pairs.fasta --output-csv results/cpu.csv
CUDA_VISIBLE_DEVICES=0 ./scripts/predict_gpu.sh --csv examples/pairs.csv --output-csv results/gpu.csv
1 maintainer
Metadata
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Release files for respepbind 0.0.1
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