content example of pathway simulation work and map pathway simulation model and equations

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: phacyz@nus.edu.sg ; 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

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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)

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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

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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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