Local descriptors of protein structure

• US 20040171063A1
• Filed: 02/27/2003
• Published: 09/02/2004
• Est. Priority Date: 02/27/2003
• Status: Abandoned Application

• Current Assignee: Lawrence Livermore National Security LLC (Government of the United States of America)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Kryshtafovych, Andriy A., Fidelis, Krzysztof A.
• Application Number:
  US10/378,492
• Publication Number:
  US 20040171063A1
• Time in Patent Office: Days
• US Class Current: 435/7.1
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment

Abstract

Information about a protein is produced by a number of steps including: Developing a specification of how local descriptors of protein structure are defined. Developing a local descriptors of protein structure database including calculated descriptors. Developing a definition of inter-descriptor similarity measure. Developing a local descriptors of protein structure class database of descriptors organized by their similarity. Producing information about any protein by analyzing said protein using the local descriptors of protein structure class database of descriptors organized by their similarity.

Claims

1. A method of producing information about a protein using a protein structure, comprising the steps of:

developing a specification of how local descriptors of protein structure are defined,

developing a local descriptors of protein structure database including calculated descriptors,

developing a definition of inter-descriptor similarity measure,

developing a local descriptors of protein structure class database of descriptors organized by their similarity, and

producing information about any protein by analyzing said protein using the local descriptors of protein structure class database of descriptors organized by their similarity.

2. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity, comprises analyzing said protein on the basis of statistics of protein sequence coverage in terms of local descriptors of protein structure class geometries.

3. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity, comprises analyzing said protein on the basis of new structure classification in terms of pre-defined local descriptors of protein structure class geometries.

4. The method of producing information about a protein of claim 1, wherein said step of developing a local descriptors of protein structure database including calculated descriptors is organized by protein fold classes, architectures, and families.

5. The method of producing information about a protein of claim 1, wherein said step of developing a local descriptors of protein structure class database of descriptors organized by their similarity is completed using said definition of inter-descriptor similarity measure.

6. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to analysis of protein structure.

7. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to superposition of protein structures and their subsets.

8. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to comparative (homology) modeling of proteins.

9. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to protein fold recognition.

10. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to structural and functional annotation of genomes.

11. The method of producing information about a protein of claim 1, wherein said step of producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to ab initio prediction of protein structure.

12. A system for producing information about a protein using a protein sequence, comprising:

means for developing a specification of how local descriptors of protein structure are defined in said protein sequence,

means for developing a local descriptors of protein structure database including calculated descriptors,

means for developing a definition of inter-descriptor similarity measure,

means for developing a local descriptors of protein structure class database of descriptors organized by their similarity, and

means for producing information about said protein by analyzing said protein using the local descriptors of protein structure class database of descriptors organized by their similarity.

13. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity, comprises a means for analyzing said protein on the basis of statistics of protein sequence coverage in terms of local descriptors of protein structure class geometries.

14. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity, comprises a means for analyzing said protein on the basis of new structure classification in terms of pre-defined local descriptors of protein structure class geometries.

15. The system for producing information about a protein of claim 12, wherein said means for developing a local descriptors of protein structure database including calculated descriptors is organized by protein fold classes, architectures, and families.

16. The system for producing information about a protein of claim 12, wherein said means for developing a local descriptors of protein structure class database of descriptors organized by their similarity is completed using said definition of inter-descriptor similarity measure.

17. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to analysis of protein structure.

18. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to superposition of protein structures and their subsets.

19. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to comparative (homology) modeling of proteins.

20. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to protein fold recognition.

21. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to structural and functional annotation of genomes.

22. The system for producing information about a protein of claim 12, wherein said means for producing information about said protein by analyzing said protein using said local descriptors of protein structure class database of descriptors organized by their similarity provides information relating to ab initio prediction of protein structure.

23. The system for producing information about a protein of claim 12, including means for predicting the structure of said protein.