A structure-based deep learning framework for protein engineering

While deep learning methods exist to guide protein optimization, examples of novel proteins generated with these techniques require a priori mutational data. Here we report a 3D convolutional neural network that associates amino acids with neighboring chemical microenvironments at state-of-the-art accuracy. This algorithm enables identification of novel gain-of-function mutations, and subsequent experiments confirm substantive phenotypic improvements in stability-associated phenotypes in vivo across three diverse proteins.