Predicting protein stability changes under multiple amino acid
  substitutions using equivariant graph neural networks
Sebastien Boyer Sam Money-Kyrle Oliver Bent
The accurate prediction of changes in protein stability under multiple amino
acid substitutions is essential for realising true in-silico protein re-design.
To this purpose, we propose improvements to state-of-the-art Deep learning (DL)
protein stability prediction models, enabling first-of-a-kind predictions for
variable numbers of amino acid substitutions, on structural representations, by
decoupling the atomic and residue scales of protein representations. This was
achieved using E(3)-equivariant graph neural networks (EGNNs) for both atomic
environment (AE) embedding and residue-level scoring tasks. Our AE embedder was
used to featurise a residue-level graph, then trained to score mutant stability
($\Delta\Delta G$). To achieve effective training of this predictive EGNN we
have leveraged the unprecedented scale of a new high-throughput protein
stability experimental data-set, Mega-scale. Finally, we demonstrate the
immediately promising results of this procedure, discuss the current
shortcomings, and highlight potential future strategies.