STRUCTURAL ALIGNMENT METHOD MAKING USE OF A DOUBLE DYNAMIC PROGRAMMING ALGORITHM

There is disclosed a structural alignment method making use of a double dynamic programming algorithm. A distance cut-off approximation is performed, and then .DELTA.N cut-off approximation is performed. An alignment is produced based on the results of the distance cut-off approximation and the .DELTA.N cut-off approximation. Subsequently, an .epsilon.-suboptimal region defined by the obtained approximate solution is determined. Further, double dynamic programing alignment on the full structural environment is performed for residue pairs within the .epsilon.-suboptimal region. The structural alignment method is simpler than conventional methods and can shorten computational time while maintaining high accuracy.