Local 3D structure around a protein's light-emitting center matters more than overall sequence for predicting brightness—and you can build interpretable models by explicitly encoding which atoms contact which chromophore regions.
This paper predicts how bright fluorescent proteins will be by analyzing their 3D structure around the light-emitting chromophore region. Instead of just looking at protein sequences, the method builds a graph of how atoms and chemical groups physically contact the chromophore, then uses machine learning to predict brightness.