Relevance of 3D Rotationally Equivariant Neural Networks for Predicting Protein-Ligand Binding Affinities

Proteins are fundamental to biological processes, mediating critical functions through precise molecular interactions. The rotational dynamics between ligand atoms and protein binding sites can significantly influence interaction efficacy by modifying spatial relationships. In our research, we present the PLAe (three-dimensional (3D) rotationally equivariant neural networks for predicting protein-ligand binding affinities) methodology. This novel model synergizes radial basis functions with e3nn networks to encapsulate the radial and angular dimensions of molecular features. Radial basis functions effectively measure interatomic distances, while e3nn-an advanced neural network utilizing spherical harmonics-maintains invariance under rotational and translational transformations. The Clebsch-Gordan coefficients are employed to integrate angular and atomic properties seamlessly. By merging radial basis and spherical harmonic elements with Clebsch-Gordan representations, our approach adeptly captures molecular rotational symmetries and interatomic interactions. The inclusion of an attention mechanism further refines the affinity predictions, ensuring a high level of precision. This integrative and sophisticated model sets a new benchmark to accurately predict protein-ligand binding affinities, leveraging intricate molecular details to enhance predictive performance.