A computer-assisted method for describing a folding conformation of a target protein sequence, the method comprising:
- (a) selecting a 3D coordinate data set of a target protein sequence from a protein structure database, wherein the target protein sequence is a consecutive sequence of amino acids, each amino acid comprises an alpha carbon, and the 3D coordinate data set comprises a coordinate of the alpha carbon of each amino acid;
- (b) inputting the 3D coordinate data set selected in (a) into a computer;
- (c) executing an element-dividing program stored in the computer to divide the target protein sequence into elements along the consecutive sequence of amino acids, wherein each element consists of five consecutive amino acids, the five consecutive amino acids consists of a first amino acid, a second amino acid, a third amino acid, a fourth amino acid, and a fifth amino acid, and when an element has a succeeding element, the second amino acid, the third amino acid, the fourth amino acid, and the fifth amino acid of the element are the first amino acid, the second amino acid, the third amino acid, and the fourth amino acid of the succeeding element, respectively;
- (d) executing an alpha carbon-identifying program stored in the computer to extract coordinates of the alpha carbons of each element from the 3D coordinate data set;
- (e) executing a plane-defining program stored in the computer to define a first plane of each element according to the coordinates of the alpha carbons of the first amino acid, the second amino acid, and the third amino acid of each element;
- (f) executing the plane-defining program to define a second plane of each element according to the coordinates of the alpha carbons of the second amino acid, the third amino acid, and the fourth amino acid of each element;
- (g) executing the plane-defining program to define a third plane of each element according to the coordinates of the alpha carbons of the third amino acid, the fourth amino acid, and the fifth amino acid of each element;
- (h) executing a torsion angle-calculating program stored in the computer to calculate a first torsion angle of each element with respect to the first plane and the second plane of each element, and to calculate a second torsion angle of each element with respect to the second plane and the third plane of each element;
- (i) executing a distance-calculating program stored in the computer to calculate a pitch distance of each element, wherein the pitch distance is a distance between the alpha carbon of the first amino acid and the alpha carbon of the fifth amino acid in each element;
- (j) executing a range-identifying program stored in the computer to identify a range of the first torsion angle, a range of the second torsion angle, and a range of the pitch distance for each element, wherein the range of the first torsion angle is a member selected from a first range group consisting of a1, a2, and a3, the range of the second torsion angle is a member selected from a second range group consisting of b1, b2, and b3, and the range of the pitch distance is a member selected from a third range group consisting of c1, c2, and c3;
- (k) executing a vector-assigning program stored in the computer to combine the range of the first torsion angle, the range of the second range angle, and the range of the pitch distance of each element obtained in (j) to obtain a Protein Folding Shape Code vector for each element;
- (l) executing the vector-assigning program to designate each Protein Folding Shape Code vector obtained in (k) with a vector letter;
- and
- (m) executing an outputting program stored in the computer to arrange the vector letters obtained in (1) in an order in accordance with the consecutive sequence of amino acids to obtain a structural assignment document for data output, wherein the structural assignment document is a description of the folding conformation of the target protein sequence.