chowdhury-lab/protein-binding-affinity

🧬 Protein Binding Affinity Predictor

Dual-head model for predicting protein-protein binding affinity (ΔG) and mutation effects (ΔΔG).

Model Performance

Metric	Validation Score
dG Pearson	0.51
ddG Pearson	0.70
Sum PCC	1.21

Architecture

• Backbone: ESM-600M (frozen embeddings)
• Pooling: Sliced-Wasserstein Embedding (SWE)
• Heads: Dual-head (dG + ddG)
• Input: Protein sequences (1153-dim = 1152 ESM + 1 mutation channel)

Usage

from huggingface_hub import hf_hub_download
import torch

# Download checkpoint
ckpt = hf_hub_download(repo_id="supanthadey1/protein-binding-affinity", filename="best_model_checkpoint.pt")
checkpoint = torch.load(ckpt, map_location='cpu')
model.load_state_dict(checkpoint['model_state_dict'])

Predictions

• ΔG (kcal/mol): Binding free energy. More negative = stronger binding.
• ΔΔG (kcal/mol): Mutation effect. Negative = stabilizing, Positive = destabilizing.

Training Data

Trained on multiple datasets including SKEMPI, BindingGym, PDBbind, and others.

Citation

If you are using Seq2Bind / TwinPeaks please cite both papers as:

Ma, X., Dey, S., Zelinski, C., Li, Q. and Chowdhury, R., 2025. Seq2Bind webserver for binding site prediction from sequences using fine-tuned protein language models. NAR Genomics and Bioinformatics, 7(4), p.lqaf154.

Dey, S. and Chowdhury, R., 2025. Twin Peaks: Dual-Head Architecture for Structure-Free Prediction of Protein-Protein Binding Affinity and Mutation Effects. arXiv preprint arXiv:2509.22950.