Field-based similarity search system and method

• US 20030009298A1
• Filed: 03/22/2002
• Published: 01/09/2003
• Est. Priority Date: 03/23/2001
• Status: Abandoned Application

• Current Assignee: GlobalFoundries, Inc.
• Original Assignee: International Business Machines Corporation
• Inventors: Huber, Wolfgang, Rice, Julia E., Pitman, Michael C., Horn, Hans W., Fitch, Blake G., Swope, William C.
• Application Number:
  US10/102,902
• Publication Number:
  US 20030009298A1
• Time in Patent Office: Days
• US Class Current: 702/27
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/20 Supervised data analysis
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16C 20/40 Searching chemical structures or physicochemical data

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.

Claims

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.

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.

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.