1. Lecture 6: Determination of Pathway Parameters Y.Z. Chen Department of Pharmacy National University of Singapore Tel: 65-6616-6877; Email: phacyz@nus.edu.sg ; Web: http://bidd.nus.edu.sg phacyz@nus.edu.sghttp://bidd.nus.edu.sgphacyz@nus.edu.sghttp://bidd.nus.edu.sgContent Example of pathway simulation work and mapExample of pathway simulation work and map Pathway simulation model and equationsPathway simulation model and equations Pathway simulation parametersPathway simulation parameters Pathway simulation parameter estimation methodsPathway simulation parameter estimation methods Sequence similarity, Global optimization (against protein concentrations), QKIRSequence similarity, Global optimization (against protein concentrations), QKIR Parameter sensitivity analysisParameter sensitivity analysis

2. Pathway Simulation Work

3. 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

15. 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. 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. Keeble, Biochemistry 45, 3243 (2006)

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

23. Ober, J Biol Chem 278, 12805 (2003)

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

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

27. Khan, J Biol Chem 281, 11702 (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. 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

46. A B C