Patent Document ID: 9864833
Application ID: 14256692
Patent Flag: 1

Claim One:
1. A method of performing artificial evolution, implemented using a nucleic acid synthesizer and a digital system comprising memory and a processor, said method comprising: (a) receiving, by the digital system, data characterizing a training set of a protein variant library, wherein the data provides an 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, by the digital system, a sequence-activity model for predicting the 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 a relative impact on the activity by an interaction of the two or more dummy independent variables, and each of the two or more dummy independent variables specifies a presence or absence of one residue or codon at a different sequence position of two or more sequence positions; (c) using the sequence-activity model to identify, by the digital system, a protein variant or a portion thereof; and (d) automatically controlling, by the digital system, the nucleic acid synthesizer to synthesize nucleic acid molecules encoding the protein variant or the portion thereof identified in (c).