Patent ID: 6125331
Filing Date: 2000-09-26
Classification: G16B

Abstract:
A structural alignment method for proteins using a double dynamic programming algorithm, the method comprising the steps of:(a) performing a first distance cut-off approximation for determining a first local environment of a first residue of a first protein centered at a side chain of said first residue of said first protein, and residues with side chain centers that are present within said first distance cut-off are selected as constituent elements of said first local environment of said first residue, wherein a number of residues in said first local environment is less than a number of residues in said first protein;performing a second distance cut-off approximation for determining a second local environment of a second residue of a second protein centered at a side chain of said second residue of said second protein, and residues with side chain centers that are present within said second distance cut-off are selected as constituent elements of said second local environment of said second residue;(b) performing .DELTA.N cut-off approximation for selectively comparing residue pairs obtained by said first and second distance cut-off approximations having a first similarity of local environments, said first similarity having a value based on a result of said step of performing .DELTA.N cut-off approximation;(c) generating a 3-dimensional structural alignment of said first protein with said second protein using results of said first and second distance cut-off approximations and said .DELTA.N cut-off approximation; and(d) outputting said 3-dimensional structural alignment indicating residue-to-residue correspondence between said first protein and said second protein,wherein said 3-dimensional structural alignment is generated so that a total sum of values of similarities for pairs of said first and second residues included in said 3-dimensional structural alignment is a maximum.