A computer-implemented method of training a neural network to improve a characteristic of a protein comprises collecting a set of amino acid sequences from a database, compiling each amino acid sequence into a three-dimensional crystallographic structure of a folded protein, training a neural network with a subset of the three-dimensional crystallographic structures, identifying, with the neural network, a candidate residue to mutate in a target protein, and identifying, with the neural network, a predicted amino acid residue to substitute for the candidate residue, to produce a mutated protein, wherein the mutated protein demonstrates an improvement in a characteristic over the target protein. A system for improving a characteristic of a protein is also described. Improved blue fluorescent proteins generated using the system are also described.