Patent ID: 7783428

Claim:
A method for identifying amino acid residues for variation in order to affect a desired activity, said method comprising: (a) receiving data characterizing a training set of a protein variant library, wherein the data comprises activity and an amino acid sequence for each protein variant in the training set; (b) from the data, developing a sequence activity model for predicting activity as a function of independent variables, each specifying the presence or absence of an amino acid residue, the identify of said amino acid residue, and the position of said amino acid residue in the sequence; (c) using the sequence activity model to rank residue positions in the sequence and residue types at the ranked residue positions in order of impact on the desired activity; (d) using the ranking to identify one or more amino acid residues, in proteins of the protein variant library or a reference amino acid sequence, that are to be varied or fixed in order to impact the desired activity; and (e) defining a new protein variant library wherein the sequences of the members of the new protein variant library comprise the identified amino acid residues varied or fixed in order to impact the desired activity, wherein operations (a)-(e) are performed by executing instructions on a computer system programmed to perform said operations.