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The metrics of the PIM^® profile consist to evaluate the 16 charge/polarity interactions identified by reading the sequence of a protein by pairs of residues, from left to right. The PIM^® system has three stages:

1 1. The amino acid sequence is converted to the numeric charge/polarity-related annotations P+, P−, N, and NP, where P+ are H, His; K, Lys; and R, Arg; P− are D, Asp; and E, Glu; N are C, Cys; G, Gly; N, Asp; Q, Gln; S, Ser; T, Thr; and Y, Tyr; and NP are A, Ala; F, Phe; I, Ile; L, Leu; M, Met; P, Pro; V, Val; and W, Trp.

2 2. The sequence is expressed in FASTA format; all the incidences of these pairs of amino acids are registered in a 4 × 4 algebraic matrix where its rows and columns are the four PIM® profile groups. Once all amino acid pairs are recorded, the incidence matrix is normalized.

3 3. Create a 16-element vector putting, from left to right, the 16 possible positions from the incidence matrix in increasing or decreasing order. Two proteins are equal if their 16-element vectors are the same.

Two proteins are equal if their 16-element vectors shared the same preponderant function.