Patent Document ID: 20140249035
Application ID: 14256692
Patent Flag: 0

Claim One:
1. A method for identifying amino acid residues for variation in 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 an amino acid sequence or a nucleic acid sequence encoding a protein variant for each protein variant in the training set; (b) from the data, developing a sequence-activity model for predicting activity as a function of multiple independent variables, the sequence activity model comprising a plurality of linear terms and one or more non-linear terms, wherein, for each non-linear term, the non-linear term comprises a coefficient and two or more dummy independent variables, the coefficient indicates the relative impact on activity by the interaction of the two or more dummy independent variables, and each of the two or more dummy independent variables specifies the presence or absence of a particular residue or codon at a specific sequence position; and (c) using the sequence-activity model to identify one or more amino acid residues or codons at specific positions for varying or fixing to impact the desired activity, wherein operations (a)-(c) are performed by executing instructions on a computer system programmed to perform said operations.