Patent ID: 7231301

Claim:
A method for predicting functional site of a functionally unknown protein obtained from an organism, in which amino acid sequences for all proteins expressed by the organism are estimated from known cDNA, said method comprises: (1) determining in the amino acid sequences from all proteins of the organism, the frequency of occurrence of each amino acid and the frequency of occurrence of individual oligopeptides produced by permutations of twenty amino acids, and determining the smallest length (n) of oligopeptides having criteria of among oligopeptides of length (n), the number of oligopeptides which occur once in all of the proteins is smaller than the number of oligopeptides which occur twice in all of the proteins, and among oligopeptides of length (n+1), the number of oligopeptides which occur once in all of the proteins is larger than the number of oligopeptides which occur twice in all of the proteins; (2) determining from all of the proteins of the organism, the frequency of occurrence of an Aji-oligopeptide of length (n+1), which is a fragment of the protein for predicting the amino-acid residues responsible for functional activity, and contains the j-th amino-acid residue Aj (n+1≦j≦L−n) from the N-terminus of the amino acid sequence (length of L) of the protein, wherein the j-th amino-acid residue Aj is the i-th residue Aji from the N-terminus of the Aji-oligopeptide, the Aji-oligopeptide is aj1aj2, . . . Aji . . . ajnaj(n+1), 1≦i≦n+1, Aj is Aji and Aj is the i-th residue of the oligopeptide, and aj1 is Aj−i+1, . . . , aj(n+1)=Aj−i+(n+1), and determining from all of the proteins of the organism, the frequency of occurrence of an Xji-oligopeptide of length (n+1), wherein the Xji-oligopeptide is aj1aj2 . . . Xji . . . ajnaj(n+1), and further wherein 1≦i≦n+1, n+1≦j≦L−n; and the i-th residue Xji is any amino acid, and aj1 is Aj−i+1, . . . , aj(n+1)=Aj−i+(n+1); (3) calculating ratio value Yji of the frequency of occurrence of the Aji-oligopeptide to that of the Xji-oligopeptide; (4) determining mean value Yj of the value Yji, wherein Yj = ∑ i = 1 n + 1 ⁢ ⁢ Yji / ( n + 1 ) , (5) determining Zj, wherein Zj value is defined as the representative value of the function of the j-th amino-acid residue Aj of the amino acid sequence (length of L), and wherein Zj=f(Yj), and function f is a monotonously decreasing function or a monotonously increasing function; and (6) repeating steps (2) to (5) sequentially and determining the Zj value of each Aj of all the amino-acid residues at positions between n+1≦j≦L−n in the amino acid sequence (length of L), thereby predicting the degree of involvement of each amino-acid residue of said sequence in the function of the protein by using Zj value as an indicator.