Mathematical processes for determination of peptidase cleavage

A computer implemented process for providing desired peptidase cleavage sites in a synthetic polypeptide comprising:

• a) obtaining an amino acid sequence for a target polypeptide;
• b) deriving an ensemble of peptidase cleavage prediction equations for each possible cleavage site dimer by:
• (i) assembling experimentally derived data comprising a multiplicity of measurements of amino acid physicochemical properties;
• (ii) producing a correlation matrix of the experimentally derived data;
• (iii) deriving by Principal Component Analysis multiple uncorrelated dimensionless, weighted and ranked proxy descriptors to describe at least 80% of the variance in said physicochemical properties of individual amino acids,
• (iv) using said proxy descriptors to describe individual amino acids in a set of peptides each of which comprises a specific cleavage site dimer experimentally determined to be cleaved, and to describe the individual amino acids in a set of peptides each of which comprises the same cleavage site dimer experimentally determined to be uncleaved;
• (v) comparing, via probabilistic modeling, the amino acid descriptors of said peptides comprising said experimentally determined cleaved and uncleaved cleavage site dimers to derive a cleavage prediction equation for said specific cleavage site dimer based on that peptide set;
• (vi) repeating the steps of (iv) and (v) multiple times, each time with a different set of peptides that comprise the same cleavage site dimer and are experimentally determined to be cleaved or not cleaved, thereby deriving an ensemble of independently derived peptidase cleavage prediction equations for said specific cleavage site dimer;
• (vii) repeating the process of (iv) to (vi) to derive ensembles of independently derived prediction equations for every possible cleavage site dimer up to a total of 400 such ensembles;
• (viii) storing said ensembles of independently derived prediction equations on a non-transitory computer readable medium;
• (c) in-putting said amino acid sequence from said target polypeptide into a computer;
• (d) applying said proxy descriptors from said Principal Component Analysis to describe individual amino acids in said target polypeptide sequence;
• (e) deriving vectors to describe a plurality of peptides of defined length in said target polypeptide;
• (f) via said computer processor applying said up to 400 ensembles of independently derived peptidase cleavage prediction equations to said plurality of peptides of defined length from said target polypeptide to predict a plurality of peptidase cleavage sites in said target polypeptide;
• (g) identifying, by consensus of the ensembles of prediction equations, the probability of cleavage at any given cleavage site dimer in said target polypeptide;
• (h) defining amino acids subsets in said target polypeptide that are predicted to be cleaved by a peptidase;
• (i) substituting one or more amino acids in the target polypeptide to change the probability of peptidase cleavage;
• (j) synthesizing a synthetic polypeptide comprising the substituted amino acids;
• and
• (k) administering said synthetic polypeptide to a subject.