Deep Local Analysis estimates effects of mutations on protein-protein interactions

The spectacular advances in protein and protein complex structure prediction hold promises for the reconstruction of interactomes at large scale at the residue resolution. Beyond determining the 3D arrangement of interacting partners, modeling approaches should be able to sense the impact of sequence variations such as point mutations on the strength of the association. In this work, we report on DLA-mutation, a novel and efficient deep learning framework for accurately predicting mutation-induced binding affinity changes. It relies on a 3D-invariant description of local 3D environments at protein interfaces and leverages the large amounts of available protein complex structures through self-supervised learning. It combines the learnt representations with evolutionary information, and a description of interface structural regions, in a siamese architecture. DLA-mutation achieves a Pearson correlation coefficient of 0.81 on a large collection of more than 2000 mutations, and its generalization capability to unseen complexes is higher than state-of-the-art methods.