Patent ID: 7231328

Claim:
A method excecuted by a computer under the control of a program, said computer including a memory for storing said program, said method comprising the steps of: providing an ensemble of related protein backbone structures; selecting a plurality of variable positions in said ensemble of related protein backbone structures; selecting a set of amino acids to computationally test at each of said variable positions in said backbone structures; applying to each protein backbone structure in said ensemble of related protein backbone structures a protein design algorithm to generate at least one variant protein sequence for each of said protein backbone structures; sampling each amino acid in said set of amino acids at each variable position in each variant protein sequence; evaluating the energetic fitness of each amino acid in said set of amino acids at each of said variable positions in each of said variant protein sequences for each of said protein backbone structures in said ensemble of related protein backbone structures; generating a probability matrix by combining said energetic fitness of each of said amino acids in each of said variant protein sequences for each of said protein backbone structures in said ensemble of related protein backbone structures to generate a total probability for each of said amino acids; and generating a combinatorial library of proteins from said probability matrix; and generating an output of the combinatorial library.