Protein design automation for protein libraries

A method for generating at least one non-naturally occurring variant protein with at least one desired characteristic relative to a target protein comprising:

• a) inputting the coordinates of said target protein into a computer;
• b) identifying a list of variable residue positions in said target protein;
• c) applying at least one scoring function to said variable positions to generate a first set of amino acid residues at each of said variable positions to generate a primary library comprising optimized variant protein sequences;
• d) identifying a set of amino acids at each of said variable residue positions in said variant protein sequences of said primary library by generating a probability distribution table of said first set;
• e) recombining non-variable positions and variable residue positions of said second set to generate a secondary library of protein sequences, wherein the set of amino acids at each of said variable residue positions is used to generate the library of protein sequences, and wherein at least one member of said secondary library is not found in said primary library;
• f) synthesizing a plurality of said secondary library protein sequences and screening said sequences to identify at least one non-naturally occurring variant protein with at least one desired characteristic.