Shallow Sand Equations: Real-Time Height Field Simulation ...
Content Example of pathway simulation work and map Pathway simulation model and equations
description
Transcript of Content Example of pathway simulation work and map Pathway simulation model and equations
![Page 1: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/1.jpg)
Lecture 6: Determination of Pathway ParametersLecture 6: Determination of Pathway Parameters Y.Z. ChenY.Z. Chen
Department of PharmacyDepartment of PharmacyNational University of SingaporeNational University of Singapore
Tel: 65-6616-6877; Email: Tel: 65-6616-6877; Email: [email protected] ; Web: ; Web: http://bidd.nus.edu.sg
ContentContent
• Example of pathway simulation work and mapExample of pathway simulation work and map
• Pathway simulation model and equations Pathway simulation model and equations
• Pathway simulation parametersPathway simulation parameters
• Pathway simulation parameter estimation methodsPathway simulation parameter estimation methods
• Sequence similarity, Global optimization (against protein Sequence similarity, Global optimization (against protein concentrations), QKIRconcentrations), QKIR
• Parameter sensitivity analysisParameter sensitivity analysis
![Page 2: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/2.jpg)
Pathway Simulation WorkPathway Simulation Work
2121 PPSS 2121 PPSS
![Page 3: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/3.jpg)
Pathway Pathway Simulation Simulation
WorkWork
2121 PPSS 2121 PPSS
Hatakeyama Biochem J 373, 451 (2003)
![Page 4: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/4.jpg)
2121 PPSS 2121 PPSS
Pathway Pathway MapMap
Hatakeyama Biochem J 373, 451 (2003)
![Page 5: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/5.jpg)
Pathway Mathematical ModelPathway Mathematical Model
2121 PPSS
Materi & Wishart Drug Discov Today 12, 295 (2007)
![Page 6: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/6.jpg)
Pathway Mathematical ModelPathway Mathematical Model
2121 PPSS
Hatakeyama Biochem J 373, 451 (2003)
![Page 7: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/7.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation EquationsPathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)
![Page 8: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/8.jpg)
2121 PPSS 2121 PPSS
Pathway Pathway Simulation Simulation EquationsEquations
Hatakeyama Biochem J 373, 451 (2003)
![Page 9: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/9.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation EquationsPathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)
![Page 10: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/10.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation ParametersPathway Simulation ParametersHatakeyama Biochem J 373, 451
(2003)
![Page 11: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/11.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation ParametersPathway Simulation Parameters
Hatakeyama Biochem J 373, 451 (2003)
![Page 12: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/12.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein PairsExploration of Similarity Protein Pairs
![Page 13: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/13.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
![Page 14: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/14.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
![Page 15: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/15.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
Shimada, Arch Biochem Biophys 435, 207 (2005)
![Page 16: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/16.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
Shimada, Arch Biochem Biophys 435, 207 (2005)
![Page 17: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/17.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
![Page 18: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/18.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
Li, J Biol Chem 337, 743 (2004)
![Page 19: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/19.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
Li, J Biol Chem 337, 743 (2004)
![Page 20: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/20.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
![Page 21: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/21.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
Keeble, Biochemistry 45, 3243 (2006)
![Page 22: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/22.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates) Exploration of Similarity Proteins (Different Substrates)
![Page 23: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/23.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)Exploration of Similarity Proteins (Different Substrates)
Ober, J Biol Chem 278, 12805 (2003)
![Page 24: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/24.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Same Substrate) Exploration of Similarity Proteins (Same Substrate)
![Page 25: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/25.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Same Substrate) Exploration of Similarity Proteins (Same Substrate)
![Page 26: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/26.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)Exploration of Similarity Proteins (Different Substrates)
![Page 27: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/27.jpg)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)Exploration of Similarity Proteins (Different Substrates)
Khan, J Biol Chem 281, 11702 (2006)
![Page 28: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/28.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exceptions: Similarity Proteins Not always Work Exceptions: Similarity Proteins Not always Work
![Page 29: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/29.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Global Optimization Method (GOM)Global Optimization Method (GOM)
Moles, Genome Research 13, 2467 (2003)
![Page 30: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/30.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Global Optimization Method (GOM)Global Optimization Method (GOM)
Moles, Genome Research 13, 2467 (2003)
Example of decision variables:protein concentrations
![Page 31: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/31.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Application of GOM to a Model PathwayApplication of GOM to a Model Pathway
Moles, Genome Research 13, 2467 (2003)
![Page 32: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/32.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Parameters and Decision Variable Values Parameters and Decision Variable Values
Moles, Genome Research 13, 2467 (2003)
![Page 33: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/33.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Pathway Simulation EquationsPathway Simulation Equations
Moles, Genome Research 13, 2467 (2003)
![Page 34: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/34.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Fitting CurvesPathway Simulation Parameter Fitting Curves
Moles, Genome Research 13, 2467 (2003)
![Page 35: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/35.jpg)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Fitting CurvesPathway Simulation Parameter Fitting Curves
Moles, Genome Research 13, 2467 (2003)
![Page 36: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/36.jpg)
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Other Studies Using GOM StrategyOther Studies Using GOM Strategy
![Page 37: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/37.jpg)
Pathway Simulation Parameter Estimation III: Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)Quantitative kinetics-Interaction Fields Relationship (QKIR)
![Page 38: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/38.jpg)
Pathway Simulation Parameter Estimation III: Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)Quantitative kinetics-Interaction Fields Relationship (QKIR)
BMC Bioinformatics 8, 373 (2007)
![Page 39: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/39.jpg)
Pathway Simulation Parameter Estimation III: Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)Quantitative kinetics-Interaction Fields Relationship (QKIR)
BMC Bioinformatics 8, 373 (2007)
![Page 40: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/40.jpg)
Pathway Simulation Parameter Estimation III: Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)Quantitative kinetics-Interaction Fields Relationship (QKIR)
BMC Bioinformatics 8, 373 (2007)
![Page 41: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/41.jpg)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
![Page 42: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/42.jpg)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
![Page 43: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/43.jpg)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
![Page 44: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/44.jpg)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
![Page 45: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/45.jpg)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
![Page 46: Content Example of pathway simulation work and map Pathway simulation model and equations](https://reader036.fdocuments.in/reader036/viewer/2022062816/568139bb550346895da15f23/html5/thumbnails/46.jpg)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
A
B
C