Lecture 6: Determination of Pathway Parameters Y.Z. Chen Department of Pharmacy National University...
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Lecture 6: Determination of Pathway Parameters Lecture 6: Determination of Pathway Parameters Y.Z. Chen Y.Z. Chen Department of Pharmacy Department of Pharmacy National University of Singapore National University of Singapore Tel: 65-6616-6877; Email: Tel: 65-6616-6877; Email: [email protected] ; Web: ; Web: http://bidd.nus.edu.sg Content Content • Example of pathway simulation work and map Example of pathway simulation work and map • Pathway simulation model and equations Pathway simulation model and equations • Pathway simulation parameters Pathway simulation parameters • Pathway simulation parameter estimation methods Pathway simulation parameter estimation methods • Sequence similarity, Global optimization (against Sequence similarity, Global optimization (against protein concentrations), QKIR protein concentrations), QKIR • Parameter sensitivity analysis Parameter sensitivity analysis
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Transcript of Lecture 6: Determination of Pathway Parameters Y.Z. Chen Department of Pharmacy National University...
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
Pathway Simulation WorkPathway Simulation Work
2121 PPSS 2121 PPSS
Pathway Pathway Simulation Simulation
WorkWork
2121 PPSS 2121 PPSS
Hatakeyama Biochem J 373, 451 (2003)
2121 PPSS 2121 PPSS
Pathway Pathway MapMap
Hatakeyama Biochem J 373, 451 (2003)
Pathway Mathematical ModelPathway Mathematical Model
2121 PPSS
Materi & Wishart Drug Discov Today 12, 295 (2007)
Pathway Mathematical ModelPathway Mathematical Model
2121 PPSS
Hatakeyama Biochem J 373, 451 (2003)
2121 PPSS 2121 PPSS
Pathway Simulation EquationsPathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)
2121 PPSS 2121 PPSS
Pathway Pathway Simulation Simulation EquationsEquations
Hatakeyama Biochem J 373, 451 (2003)
2121 PPSS 2121 PPSS
Pathway Simulation EquationsPathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)
2121 PPSS 2121 PPSS
Pathway Simulation ParametersPathway Simulation ParametersHatakeyama Biochem J 373, 451
(2003)
2121 PPSS 2121 PPSS
Pathway Simulation ParametersPathway Simulation Parameters
Hatakeyama Biochem J 373, 451 (2003)
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein PairsExploration of Similarity Protein Pairs
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
2121 PPSS 2121 PPSS
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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)
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)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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)
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)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates) Exploration of Similarity Proteins (Different Substrates)
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)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Same Substrate) Exploration of Similarity Proteins (Same Substrate)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Same Substrate) Exploration of Similarity Proteins (Same Substrate)
Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Proteins (Different Substrates)Exploration of Similarity Proteins (Different Substrates)
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)
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
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)
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
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)
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)
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)
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)
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)
Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Other Studies Using GOM StrategyOther Studies Using GOM Strategy
Pathway Simulation Parameter Estimation III: Pathway Simulation Parameter Estimation III: Quantitative kinetics-Interaction Fields Relationship (QKIR)Quantitative kinetics-Interaction Fields Relationship (QKIR)
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)
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)
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)
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis
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