Politecnico di Torino · M3B Lab
Politecnico di TorinoM3B Lab
Protein–Ligand Kinetics - ML

Prediction of dissociation rate constants for protein–ligand complexes.

A regression model that estimates the off-rate koff of a protein–ligand complex directly from a ligand SMILES and an amino-acid sequence. Inputs are embedded with ProtBERT and ChemBERTa and passed through a regressor trained on curated kinetic data.

Input

Provide a single ligand SMILES and one or more protein chains.

Canonicalised server-side via RDKit.

One-letter codes. Separate chains with '|'. ProtBERT limit: 512 residues.

First prediction after a quiet period may take 30–60 s while the inference engine warms.

How to cite

If you use this prediction tool in your research, please cite the following publication:

@article{zizzi2026kinetics,
  title     = {Kinetics Beyond Pose: A Structure-independent Framework for koff Prediction Across Diverse Protein Families},
  author    = {Zizzi, Eric A. and Cicero, Giuseppe and Gentile, Francesco and Deriu, Marco A.},
  journal   = {ChemRxiv},
  publisher = {American Chemical Society},
  year      = {2026},
  doi       = {10.26434/chemrxiv.15003308/v1},
  url       = {https://doi.org/10.26434/chemrxiv.15003308/v1},
  note      = {Preprint. Related code: https://github.com/m3b-lab/KineticsBeyondPose},
}