Field-based similarity search system and method

Abstract

A field-based similarity search system and method includes a database for storing at least one candidate molecule, an input device for inputting a query molecule, and a processor for identifying a candidate molecule which is similar to the query molecule based on a similarity of fragment pair features.

What is claimed is:  
     
         1 . A field-based similarity search system, comprising: 
 a database for storing at least one candidate molecule;    an input device for inputting a query molecule; and    a processor for identifying a candidate molecule which is similar to said query molecule based on a similarity of fragment pair features.    
     
     
         2 . The system according to  claim 1 , wherein said processor identifies a feature of a query molecule fragment pair.  
     
     
         3 . The system according to  claim 2 , wherein said processor matches a query molecule fragment pair feature with a candidate molecule fragment pair feature.  
     
     
         4 . The system according to  claim 3 , wherein said processor retrieves a candidate molecule fragment pair having at least a predetermined number of matching features.  
     
     
         5 . The system according to  claim 1 , wherein said processor aligns retrieved fragment pairs using a pose clustering method.  
     
     
         6 . The system according to  claim 1 , wherein said processor constructs a fully aligned candidate molecule by assembling retrieved fragment pairs.  
     
     
         7 . The system according to  claim 1 , wherein said processor generates said fragment pair for said query molecule.  
     
     
         8 . The system according to  claim 1 , further comprising: 
 a memory device for storing said query molecule fragment pair feature.    
     
     
         9 . The system according to  claim 8 , wherein said memory device stores data and instructions to be executed by said processor.  
     
     
         10 . The system according to  claim 1 , wherein said fragment pair comprises two neighboring fragments connected by a rotatable bond at a specific dihedral angle.  
     
     
         11 . The system according to  claim 1 , wherein said feature comprises a generalization of a CoMMA descriptor.  
     
     
         12 . The system according to  claim 1 , further comprising: 
 a display device for displaying an output from said processor.    
     
     
         13 . A similarity search method, comprising 
 generating a conformational space representation and an arbitrary description of a three-dimensional property field for a flexible molecule;    characterizing parts of said flexible molecule and representing a query molecule using said arbitrary description for a comparison with said conformational space representation; and    aligning said parts to said query molecule and assembling said parts to form an alignment onto said query molecule.    
     
     
         14 . A similarity search method, comprising 
 identifying a feature of a query molecule fragment pair;    matching a query molecule fragment pair feature with a candidate molecule fragment pair feature; and    retrieving a candidate molecule fragment pair having at least a predetermined number of matching features.    
     
     
         15 . A method for finding alignments of a flexible molecule to a query molecule comprising: 
 representing a conformation space of said flexible molecule;    generating an arbitrary description of a three-dimensional property field of said flexible molecule;    characterizing parts of said flexible molecule using said arbitrary description;    representing a query molecule using said arbitrary description for a comparison with molecules represented by said conformation space;    aligning said parts of said flexible molecule to said query molecule; and    assembling said parts of said flexible molecule to form an alignment thereof onto said query molecule.    
     
     
         16 . A programmable storage medium tangibly embodying a program of machine-readable instructions executable by a digital processing apparatus to perform a similarity search method, said method comprising: 
 generating a conformational space representation and an arbitrary description of a three-dimensional property field for a flexible molecule;    characterizing parts of said flexible molecule and representing a query molecule using said arbitrary description for a comparison with said conformational space representation; and    aligning said parts to said query molecule and assembling said parts to form an alignment onto said query molecule.    
     
     
         17 . The method according to  claim 14 , further comprising: 
 storing said query molecule fragment pair feature.    
     
     
         18 . The method according to  claim 17 , further comprising: 
 storing data and instructions to be executed by said processor.    
     
     
         19 . The method according to  claim 14 , wherein said fragment pair comprises two neighboring fragments connected by a rotatable bond at a specific dihedral angle.  
     
     
         20 . The method according to  claim 14 , wherein said feature comprises a generalization of a CoMMA descriptor.