Patent ID: 7136760

Claim:
A computer implemented method for predicting and modeling RNA pseudoknot structures, the method comprising the steps of: (a) setting criteria required for modeling RNA pseudoknots; (b) setting structural elements and data structures for representing a whole RNA structure containing pseudoknots; (c) determining an input format for modeling and a drawing order of the structure; (d) determining connectivity relations between regular loops and stems in the structure and between pseudoknot loops (PK loops) and stems in the structure; (e) calculating radii of the regular loops and the PK loops; (f) calculating coordinates of bases in the regular loops; (g) setting internal angles of the PK loops; (h) calculating startAngles of the regular loops and angles of the stems; (i) determining positions of the pseudoknots in the PK loops; and, (j) modeling by drawing the pseudoknots and the whole RNA structure containing the pseudoknots.