1. Lecture 6: Determination of Pathway Parameters Y. Z
Lecture 6: Determination of Pathway Parameters Y.Z. Chen Department of Pharmacy National University of Singapore Tel: ; ; Web:
Content
Example of pathway simulation work and map
Pathway simulation model and equations
Pathway simulation parameters
Pathway simulation parameter estimation methods
Sequence similarity, Global optimization (against protein concentrations), QKIR
Parameter sensitivity analysis

2. Pathway Simulation Work

3. Pathway Simulation Work
Hatakeyama Biochem J 373, 451 (2003)

4. Pathway Map
Hatakeyama Biochem J 373, 451 (2003)

5. Pathway Mathematical Model
Materi & Wishart
Drug Discov Today 12, 295 (2007)

6. Pathway Mathematical Model
Hatakeyama Biochem J 373, 451 (2003)

7. Pathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)

8. Pathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)

9. Pathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)

10. Pathway Simulation Parameters
Hatakeyama Biochem J 373, 451 (2003)

11. Pathway Simulation Parameters
Hatakeyama Biochem J 373, 451 (2003)

12. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs

13. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs

14. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs

15. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs
Shimada, Arch Biochem Biophys 435, 207 (2005)

16. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs
Shimada, Arch Biochem Biophys 435, 207 (2005)

17. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs

18. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs
Li, J Biol Chem 337, 743 (2004)

19. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs
Li, J Biol Chem 337, 743 (2004)

20. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs

21. Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs
Keeble, Biochemistry 45,
3243 (2006)

22. Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)

23. Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)
Ober, J Biol Chem 278, (2003)

24. Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Same Substrate)

25. Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Same Substrate)

26. Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)

27. Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)
Khan, J Biol Chem 281, (2006)

28. Pathway Simulation Parameter Estimation I: Exceptions: Similarity Proteins Not always Work

29. Pathway Simulation Parameter Estimation II: Global Optimization Method (GOM)
Moles, Genome Research 13, 2467 (2003)

30. Pathway Simulation Parameter Estimation II: Global Optimization Method (GOM)
Moles, Genome Research 13, 2467 (2003)
Example of
decision
variables:
protein
concentrations

31. Pathway Simulation Parameter Estimation II: Application of GOM to a Model Pathway
Moles, Genome Research 13, 2467 (2003)

32. Pathway Simulation Parameter Estimation II: Parameters and Decision Variable Values
Moles, Genome Research 13, 2467 (2003)

33. Pathway Simulation Parameter Estimation II: Pathway Simulation Equations
Moles, Genome Research 13,
2467 (2003)

34. Pathway Simulation Parameter Estimation II: Pathway Simulation Parameter Fitting Curves
Moles, Genome
Research 13,
2467 (2003)

35. Pathway Simulation Parameter Estimation II: Pathway Simulation Parameter Fitting Curves
Moles, Genome
Research 13,
2467 (2003)

36. Pathway Simulation Parameter Estimation II: Other Studies Using GOM Strategy

37. Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)

38. Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)
BMC Bioinformatics
8, 373 (2007)

39. Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)
BMC Bioinformatics 8, 373 (2007)

40. Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)
BMC Bioinformatics 8, 373 (2007)

41. Pathway Simulation Parameter Sensitivity Analysis

42. Pathway Simulation Parameter Sensitivity Analysis

43. Pathway Simulation Parameter Sensitivity Analysis

44. Pathway Simulation Parameter Sensitivity Analysis

45. Pathway Simulation Parameter Sensitivity Analysis

46. Pathway Simulation Parameter Sensitivity AnalysisC A B