System for identifying and developing individual naturally-occurring proteins as food ingredients by machine learning and database mining combined with empirical testing for a target food function

A method of identifying and developing individual naturally occurring proteins as food ingredients, the method comprising:

• (a) training a computer system to predict whether an individual protein has a preselected target food function from structural characteristics and properties of the protein,
• wherein the target food function is a desired effect of the individual protein on a commercial food product when incorporated into the food product as an ingredient,
• wherein the structural characteristics and properties of the protein used to train the computer system include at least the protein's amino acid sequence,
• wherein the computer system is trained by a process of machine learning that comprises inputting into the computer system a training data set that contains said characteristics and properties for a plurality of individual proteins known to have the target food function and for a plurality of individual proteins known not to have the target food function;
• (b) applying the computer system trained in step (a) to a database that contains said characteristics and properties for each of a plurality of naturally occurring individual proteins for which it is not previously known whether the individual proteins have the target food function, thereby predicting which of the naturally occurring individual proteins in the database have the target food function;
• (c) identifying or ranking by the computer system the naturally occurring individual proteins predicted in step (b) to have the target food function, thereby obtaining a set of protein candidates;
• (d) recombinantly expressing and purifying each of the protein candidates;
• (e) conducting assays to determine or quantify which of the expressed protein candidates have the target food function;
• (f) adding structural data and/or assay results for the protein candidates tested in step (e) into the training data set;
• (g) selecting one or more of the individual proteins assayed in step (e) as potential food ingredients if they are determined in step (e) as having the target food function above a chosen threshold;
• (h) performing additional cycle(s) of steps (a) to (g) until a desired number of individual proteins have been selected as potential food ingredients having the target food function above the threshold;
• and then
• (i) assessing one or more individual proteins selected as potential food ingredients in step (h) to determine whether it meets desired performance requirements as part of a food preparation.