Computational methods and systems for improving cell-mediated immune response

• US 20070265819A1
• Filed: 05/25/2007
• Published: 11/15/2007
• Est. Priority Date: 08/24/2004
• Status: Abandoned Application

• Current Assignee: Deep Science LLC (Intellectual Ventures LLC)
• Original Assignee: Searete LLC (Intellectual Ventures LLC)
• Inventors: Jung, Edward, Wilson, Richa, Sweeney, Elizabeth, Bangera, Mahalaxmi, Myhrvold, Nathan, Wood, Lowell, Ishikawa, Muriel
• Application Number:
  US11/807,336
• Publication Number:
  US 20070265819A1
• Time in Patent Office: Days
• US Class Current: 703/11
• CPC Class Codes: A61K 39/00 Medicinal preparations containing antigens or antibodies materials for immunoassay G01N33/53

Abstract

The present application relates, in general, to a system and/or method related to detection and/or treatment.

Claims

1. A system comprising:

at least one computer program for use with at least one computer system and wherein the computer program includes a plurality of instructions including but not limited to;

one or more instructions for designating one or more computable epitopes of at least one agent;

one or more instructions for predicting one or more changes in the one or more computable epitopes of the at least one agent; and

one or more instructions for aiding identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent.

2. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for associating at least one of the one or more computable epitopes with an evocation of at least a part of an immune response in a host.

3. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for designating at least one meta-signature.

4. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for associating at least one of the one or more computable epitopes with display by the at least one agent.

5. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for designating at least one computable immunogenic epitope of the at least one agent.

6. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for designating at least one lipid, peptide, glycoprotein, carbohydrate, sugar, portion thereof or combination thereof.

7. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for designating one or more computable epitopes arising from a substantially non-linear form.

8. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for designating one or more computable epitopes arising from at least one form of nontypical processing.

9. The system of claim 8, wherein the at least one form of nontypical processing includes at least one of:

autophagy, transport, proteasomal processing, cross-presentation, or extra-proteasomal processing.

10. The system of claim 1, wherein the one or more instructions for designating one or more computable epitopes of at least one agent further comprises:

one or more instructions for designating one or more computable epitopes arising from at least one antigen not entirely composed of protein.

11. The system of claim 1, wherein the one or more instructions for predicting one or more changes in the one or more computable epitopes of the at least one agent further comprises:

one or more instructions for associating the one or more computable epitopes with at least one disease state.

12. The system of claim 1, wherein the one or more instructions for aiding identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent further comprises:

one or more instructions for providing one or more predicted courses of an immune response in a host.

13. The system of claim 1, further comprising:

one or more instructions for aiding identification of one or more epitopes with a probable sequence match to a host sequence.

14. The system of claim 1, further comprising:

one or more instructions for designating at least one of the one or more computable epitopes having a substantially similar structural match with an entity.

15. The system of claim 1, further comprising:

one or more instructions for ranking the one or more computable epitopes of the at least one agent.

16. The system of claim 1, further comprising:

one or more instructions for associating at least one of the one or more computable epitopes of the at least one agent with at least a part of a progression of an immune response in a host.

17. The system of claim 1, further comprising:

one or more instructions for associating the one or more computable epitopes of the at least one agent with at least one disease state.

18. The system of claim 1, further comprising:

one or more instructions for associating at least one group of the one or more computable epitopes with at least one user chosen parameter.

19. A system, comprising:

circuitry for designating one or more computable epitopes of at least one agent;

circuitry for predicting one or more changes in the one or more computable epitopes of the at least one agent; and

circuitry for aiding identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent.

20. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for associating at least one of the one or more computable epitopes with an evocation of at least a part of an immune response in a host.

21. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for designating at least one meta-signature.

22. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for associating at least one of the one or more computable epitopes with display by the at least one agent.

23. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for designating at least one computable immunogenic epitope of the at least one agent.

24. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for designating at least one lipid, peptide, glycoprotein, carbohydrate, sugar, portion thereof or combination thereof.

25. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for designating one or more computable epitopes arising from a substantially non-linear form.

26. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for designating one or more computable epitopes arising from at least one form of nontypical processing.

27. The system of claim 26, wherein the at least one form of nontypical processing includes at least one of:

autophagy, transport, proteasomal processing, cross-presentation, or extra-proteasomal processing.

28. The system of claim 19, wherein the circuitry for designating one or more computable epitopes of at least one agent further comprises:

circuitry for designating one or more computable epitopes arising from at least one antigen not entirely composed of protein.

29. The system of claim 19, wherein the circuitry for predicting one or more changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for associating the one or more computable epitopes with at least one disease state.

30. The system of claim 19, wherein the circuitry for aiding identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent further comprises:

circuitry for providing one or more predicted courses of an immune response in a host.

31. The system of claim 19, further comprising:

circuitry for aiding identification of one or more epitopes with a probable sequence match to a host sequence.

32. The system of claim 19, further comprising:

circuitry for designating at least one of the one or more computable epitopes having a substantially similar structural match with an entity.

33. The system of claim 19, further comprising:

circuitry for ranking the one or more computable epitopes of the at least one agent.

34. The system of claim 19, further comprising:

circuitry for associating at least one of the one or more computable epitopes of the at least one agent with at least a part of a progression of an immune response in a host.

35. The system of claim 19, further comprising:

circuitry for associating the one or more computable epitopes of the at least one agent with at least one disease state.

36. The system of claim 19, further comprising:

circuitry for associating at least one group of the one or more computable epitopes with at least one user chosen parameter.

37. A method, comprising:

designating one or more computable epitopes of at least one agent;

predicting one or more changes in the one or more computable epitopes of the at least one agent; and

aiding identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent.

38. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

associating at least one of the one or more computable epitopes with an evocation of at least a part of an immune response in a host.

39. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

designating at least one meta-signature.

40. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

associating at least one of the one or more computable epitopes with display by the at least one agent.

41. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

designating at least one computable immunogenic epitope of the at least one agent.

42. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

designating at least one lipid, peptide, glycoprotein, carbohydrate, sugar, portion thereof or combination thereof.

43. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

designating one or more computable epitopes arising from a substantially non-linear form.

44. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

designating one or more computable epitopes arising from at least one form of nontypical processing.

45. The method of claim 44, wherein the at least one form of nontypical processing includes at least one of:

autophagy, transport, proteasomal processing, cross-presentation, or extra-proteasomal processing.

46. The method of claim 37, wherein designating one or more computable epitopes of at least one agent further comprises:

designating one or more computable epitopes arising from at least one antigen not entirely composed of protein.

47. The method of claim 37, wherein predicting one or more changes in the one or more computable epitopes of the at least one agent further comprises:

associating the one or more computable epitopes with at least one disease state.

48. The method of claim 37, wherein aiding identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent further comprises:

providing one or more predicted courses of an immune response in a host.

49. The method of claim 37, further comprising:

aiding identification of one or more epitopes with a probable sequence match to a host sequence.

50. The method of claim 37, further comprising:

designating at least one of the one or more computable epitopes having a substantially similar structural match with an entity.

51. The method of claim 37, further comprising:

ranking the one or more computable epitopes of the at least one agent.

52. The method of claim 37, further comprising:

associating at least one of the one or more computable epitopes of the at least one agent with at least a part of a progression of an immune response in a host.

53. The method of claim 37, further comprising:

associating the at least one or more computable epitopes of the at least one agent with at least one disease state.

54. The method of claim 37, further comprising:

associating at least one group of the one or more computable epitopes with at least one user chosen parameter.