Computational methods and systems to reinforce a humoral immune response

• US 20070288173A1
• Filed: 03/26/2007
• Published: 12/13/2007
• Est. Priority Date: 08/24/2004
• Status: Abandoned Application

• Current Assignee: Deep Science LLC (Intellectual Ventures LLC)
• Original Assignee: Searete LLC A Limited Liability Corporation of The State of Delaware
• Inventors: Wilson, Richa, Myhrvold, Nathan, Bangera, Mahalaxmi, Jung, Edward, Ishikawa, Muriel, Wood, Lowell, Sweeney, Elizabeth
• Application Number:
  US11/728,950
• Publication Number:
  US 20070288173A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G01N 33/6878 in eptitope analysis
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/30 Detection of binding sites or motifs
• CPC Class Codes: G16B 20/50 Mutagenesis
• 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

Abstract

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

Claims

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

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

designating one or more computable epitopes of at least nine nucleotides.

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

designating at least a portion of at least one of a nucleotide, a carbohydrate, a lipid, a polysaccharide, a lipopolysaccharide, a glycolipid, a glycoprotein, and/or a polyglycopeptide.

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

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

9. The method of claim 1, wherein the predicting one or more changes in the one or more computable epitopes of the at least one agent further comprises:

designating the one or more computable epitopes having a substantially similar functional sequence match with at least one host.

10. The method of claim 1, wherein the predicting one or more changes in the one or more computable epitopes of the at least one agent further comprises:

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

11. The method of claim 1, wherein the aiding the 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 and wherein the one or more predicted courses are responsive to one or more interventions.

12. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a part of one or more of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

13. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a part of at least one B-lymphocyte.

14. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least one modulator of at least a part of a B-lymphocyte.

15. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more of a modulator of at least a part of at least one of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

16. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least a part of one or more of a humanized antibody.

17. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more of a modulator of at least a part of at least one of a humanized antibody.

18. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of one or more immune response components directed to at least one of a glycoprotein, and/or a receptor ligand.

19. The method of claim 1, wherein the aiding the identification of one or more immune response components associated with the one or more computable epitopes of the at least one agent includes:

aiding the identification of at least one modulator of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent.

20. The method of claim 19, wherein the at least one modulator of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent, further comprises:

aiding the identification of at least one suppressor of mutational alteration of the at least one agent.

21. The method of claim 19, wherein the at least one modulator of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent, further comprises:

aiding the identification of at least one interfering nucleic acid or nucleic acid sequence.

5. (canceled)

6. (canceled)

7. (canceled)

8. (canceled)

22. A method, comprising:

identifying an association of at least a computable portion of one or more agents with at least a part of an immune response;

projecting a pattern of one or more changes relating to the at least a computable portion of the one or more agents; and

selecting one or more immune response components in response to the projecting.

23. The method of claim 22, wherein the selecting one or more immune response components further comprises:

selecting at least a part of one or more of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

24. The method of claim 22, wherein the selecting one or more immune response components further comprises:

selecting one or more modulators of at least a part of at least one of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

25. The method of claim 22, wherein the selecting one or more immune response components further comprises:

selecting at least a part of at least one B-lymphocyte.

26. The method of claim 22, wherein the selecting one or more immune response components further comprises:

selecting one or more modulators of at least a part of at least one B-lymphocyte.

27. The method of claim 22, wherein the selecting one or more immune response components further comprises:

selecting at least a part of one or more humanized antibody.

28. The method of claim 22, wherein the selecting one or more immune response components further comprises:

selecting one or more of a modulator of at least a part of at least one humanized antibody.

29. The method of claim 22, wherein the identifying an association of at least a computable portion of one or more agents with at least a part of an immune response further comprises:

identifying an association of at least a computable portion of at least one of a polyglycopeptide, a polysaccharide, a nucleic acid, or a toxin.

30. A system, comprising:

circuitry for identifying an association of at least a computable portion of one or more agents with at least a part of an immune response;

circuitry for projecting a pattern of one or more changes relating to the at least a computable portion of the one or more agents; and

circuitry for selecting one or more immune response components in response to said circuitry for projecting.

31. The system of claim 30, wherein the circuitry for selecting one or more immune response components further comprises:

circuitry for selecting at least a part of one or more of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

32. The system of claim 30, wherein the circuitry for selecting one or more immune response components further comprises:

circuitry for selecting one or more modulators of at least a part of at least one of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

33. The system of claim 30, wherein the circuitry for selecting one or more immune response components further comprises:

circuitry for selecting at least a part of at least one B-lymphocyte.

34. The system of claim 30, wherein the circuitry for selecting one or more immune response components further comprises:

circuitry for selecting one or more modulators of at least a part of at least one B-lymphocyte.

35. The system of claim 30, wherein the circuitry for selecting one or more immune response components further comprises:

circuitry for selecting at least a part of one or more humanized antibody.

36. The system of claim 30, wherein the circuitry for selecting one or more immune response components further comprises:

circuitry for selecting one or more modulators of at least a part of at least one humanized antibody.

37. The system of claim 30, wherein the circuitry for identifying an association of at least a computable portion of one or more agents with at least a part of an immune response further comprises:

circuitry for identifying an association of at least a portion of at least one of a polyglycopeptide, a polysaccharide, a nucleic acid, or a toxin.

38. (canceled)

39. (canceled)

40. A method, comprising:

identifying an association of at least one computable epitope of one or more agents with at least a part of an immune response;

projecting a pattern of one or more changes relating to the at least one computable epitope of the one or more agents; and

selecting one or more immune response components in response to the projecting.

41. The method of claim 40, wherein the selecting one or more immune response components further comprises:

selecting at least a part of one or more of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

42. The method of claim 40, wherein the selecting one or more immune response components further comprises:

selecting one or more modulators of at least a part of at least one of a T-lymphocyte, a killer T-lymphocyte, a helper T-lymphocyte, a cytotoxic T-lymphocyte, a T-8 lymphocyte, a Cluster of Differentiation (CD) molecule, a CD3 molecule, or a CD1 molecule.

43. The method of claim 40, wherein the selecting one or more immune response components further comprises:

selecting at least a part of at least one B-lymphocyte.

44. The method of claim 40, wherein the selecting one or more immune response components further comprises:

selecting one or more modulators of at least a part of at least one B-lymphocyte.

45. The method of claim 40, wherein the selecting one or more immune response components further comprises:

selecting at least a part of one or more humanized antibody.

46. The method of claim 40, wherein the selecting one or more immune response components further comprises:

selecting one or more modulators of at least a part of at least one humanized antibody.

47. The method of claim 40, wherein the identifying an association of at least one computable epitope of one or more agents with a part of an immune response further comprises:

identifying an association of at least one computable epitope of at least one of a polyglycopeptide, a polysaccharide, a nucleic acid, or a toxin.

48. (canceled)

49. (canceled)

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52. (canceled)

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54. (canceled)