Computer-based method for designing stablized proteins

Claim 1

A computer based method for evaluating a protein's structure to determine whether said protein contains at least two target amino acid residues, replacement of at least one of which with a cysteine residue would be sufficient to permit formation of at least one potentially protein-stabilizing disulfide bond; said method comprising the steps: (1) examining each selected pair of amino acid residues in said protein to determine if they contain certain atoms whose relative three-dimensional positions possess a geometric conformation similar to a geometric conformation possessed by atoms of a disulfide bond, (2) examining any pair of amino acids found to contain said certain atoms identified in step (1) to determine whether said disulfide bond can be accommodated without creating unacceptable steric hindrance, (3) permitting an expert operator (i) to view any possible disulfide bond which can be accommodated without creating unacceptable steric hindrance, and (ii) to rank said viewed possible disulfide bond from most likely to stabilize an engineered protein to least likely to stabilize said protein, and (4) evaluating said ranked possible disulfide bond according to expert rule criterion.