Patent ID: 7917303

Claim:
A method for identifying a combination of motifs which do not mutate simultaneously in a set of sequences and which correspond to a potential drug target on a viral polypeptide or a potential drug binding site for docking on a viral polypeptide comprising: a) selecting a set of viral sequences from a databank of viral polypeptides, b) aligning the set of viral sequences of ordered motifs represented by a single-character code on a programmed computer using a multiple sequence alignment program, c) comparing a reference viral sequence with the set of aligned viral sequences by, forming a first numerical matrix A of dimensions N×M in which N designates a number of viral sequences and M designates a number of motifs of one viral sequence of said alignment, with value A i,j being equal to a first value A1 when the motif of position i of viral sequence j with a value ranging from 0 to N is mutated in relation to a motif of position i of the reference viral sequence and equal to a second value A2 in other cases, forming two analysis matrices B and C of mutations in which: a matrix B of unmutated couples, of couples which do not mutate simultaneously, of dimension M×M, value B i,k =B k,i being equal: to a first value B1 when A i,j =A k,j =A1 irrespective of the value of j ranging from 0 to N, to a second value B2 in other cases; a matrix C of mutated couples of dimension M×M, value C k,i =C i,k being equal: to a second value C1 when A i,j =A k,j irrespective of the value of j ranging from 0 to N, to a first value C2 in other cases; determining for a set E of positions a coefficient R E whose value is R 1 when values B i,k are equal to a second value B2, irrespective of the values of i and k belonging to set E of said positions, determining for a set F of positions, a coefficient R F , the value of which is R 1 when values C i,k are equal to second value C2, irrespective of the values of i and k belonging to set F of said position; wherein the matrices i and k designate positions and j designates a sequence; d) identifying motifs not having mutated simultaneously or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of said set, e) selecting a combination of the identified motifs which are less than 20 Å apart in a three-dimensional structure of the viral polypeptide, and f) identifying the selected combination of motifs, wherein the selected combination of motifs is a combination of amino acid residues; whereby said method allows the identification of motifs corresponding to a potential drug target on a viral polypeptide or a potential drug binding site for docking on a viral polypeptide.