Method and apparatus for extracting and evaluating mutually similar portions in one-dimensional sequences in molecules and/or three-dimensional structures of molecules

Abstract

In the analysis of one-dimensional sequences of molecules, the longest common subsequence, the number of elements constituting the subsequence, and appearance positions of the subsequence are determined by a novel and simple method, and processes, such as homology decision, homology search, motif search and alignment are performed based on the results. In the analysis of these-dimensional structures of molecules, limiting conditions, such as geometrical arrangements of elements, are introduced to realize the determination of correspondence of three-dimensional structures at high speeds, and whereby it is made possible to achieve such processing as superposed display of three-dimensional structure of molecules, retrieval of three-dimensional structure, and evaluation of functions. Moreover, the molecules are divided into secondary structure that are then related to each other based on spatial similarity among the secondary structures. Furthermore, similarity among the molecules is decided based on a relationship of spatial positions of the corresponding secondary structures.

1 - 21 . (canceled)  
     
     
         22 . An apparatus for analyzing three-dimensinal structures including a first structure expressed by three dimensional coordinates of elements belonging to a first point set and a second structure expressed b three-dimensional coordinates of elements belonging to a second point set, comprising: 
 a first unit to divide the second point set into a plurality of subsets having a size that is determined by the size of the first point set;    a second unit to generate a combination of corespondence satisfying a restriction condition between the elements belonging to the first point set and the elements belonging to each of the subsets of the second point set from among all candidates for th combination of correspondence; and    a third unit to calculate a root mean square distance between the elements corresponding in the combination of correspondence generated by the second.    
     
     
         23 . (canceled)