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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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Lecture 6: Determination of Pathway Parameters Y.Z. Chen Department of Pharmacy National University of Singapore Tel: 65-6616-6877; Email: [email protected] ; Web: http://bidd.nus.edu.sg. Content Example of pathway simulation work and map Pathway simulation model and equations - PowerPoint PPT Presentation

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Page 1: 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: [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

mailto:[email protected]
http://bidd.nus.edu.sg/
Page 2: Content Example of pathway simulation work and map Pathway simulation model and equations

Pathway Simulation WorkPathway Simulation Work

2121 PPSS 2121 PPSS

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Pathway Pathway Simulation Simulation

WorkWork

2121 PPSS 2121 PPSS

Hatakeyama Biochem J 373, 451 (2003)

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2121 PPSS 2121 PPSS

Pathway Pathway MapMap

Hatakeyama Biochem J 373, 451 (2003)

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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

Pathway Mathematical ModelPathway Mathematical Model

2121 PPSS

Hatakeyama Biochem J 373, 451 (2003)

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2121 PPSS 2121 PPSS

Pathway Simulation EquationsPathway Simulation Equations

Hatakeyama Biochem J 373, 451 (2003)

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2121 PPSS 2121 PPSS

Pathway Pathway Simulation Simulation EquationsEquations

Hatakeyama Biochem J 373, 451 (2003)

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2121 PPSS 2121 PPSS

Pathway Simulation EquationsPathway Simulation Equations

Hatakeyama Biochem J 373, 451 (2003)

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2121 PPSS 2121 PPSS

Pathway Simulation ParametersPathway Simulation ParametersHatakeyama Biochem J 373, 451

(2003)

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2121 PPSS 2121 PPSS

Pathway Simulation ParametersPathway Simulation Parameters

Hatakeyama Biochem J 373, 451 (2003)

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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

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

2121 PPSS 2121 PPSS

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

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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

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

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

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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)

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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

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

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)

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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

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)

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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

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

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

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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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

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Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Global Optimization Method (GOM)Global Optimization Method (GOM)

Moles, Genome Research 13, 2467 (2003)

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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

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)

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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)

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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)

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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)

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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)

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Pathway Simulation Parameter Estimation II:Pathway Simulation Parameter Estimation II:Other Studies Using GOM StrategyOther Studies Using GOM Strategy

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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

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

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

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)

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Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis

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Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis

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Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis

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Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis

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Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis

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Pathway Simulation Parameter Sensitivity Analysis Pathway Simulation Parameter Sensitivity Analysis

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