Patent Document ID: 20070239364
Application ID: 11706034
Patent Flag: 0

Claim One:
1. A method for identifying nucleotides for variation in nucleic acids encoding a protein variant library 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 provides activity and nucleotide sequence information for each protein variant in the training set; (b) from the data, developing a sequence activity model that predicts activity as a function of nucleotide types and corresponding position in the nucleotide sequence, wherein the sequence-activity model includes one or more non-linear terms, each representing an interaction between two or more amino acid residues in the protein sequence; and (c) using the sequence activity model to rank positions in a nucleotide sequence and/or nucleotide types at specific positions in the nucleotide sequence in order of impact on the desired activity; (d) using the ranking to identify one or more nucleotides, in the nucleotide sequence, that are to be varied or fixed in order to impact the desired activity.