Accurate Prediction of Ligand-Protein Interaction Affinities with
  Fine-Tuned Small Language Models
Authors: name: Ben Fauber
Published: 2024-06-27 13:04:58

Abstract: We describe the accurate prediction of ligand-protein interaction (LPI)
affinities, also known as drug-target interactions (DTI), with instruction
fine-tuned pretrained generative small language models (SLMs). We achieved
accurate predictions for a range of affinity values associated with
ligand-protein interactions on out-of-sample data in a zero-shot setting. Only
the SMILES string of the ligand and the amino acid sequence of the protein were
used as the model inputs. Our results demonstrate a clear improvement over
machine learning (ML) and free-energy perturbation (FEP+) based methods in
accurately predicting a range of ligand-protein interaction affinities, which
can be leveraged to further accelerate drug discovery campaigns against
challenging therapeutic targets.