content example of pathway simulation work and map pathway simulation model and equations
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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 PresentationTRANSCRIPT
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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
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Pathway Simulation WorkPathway Simulation Work
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Pathway Pathway Simulation Simulation
WorkWork
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Hatakeyama Biochem J 373, 451 (2003)
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Pathway Pathway MapMap
Hatakeyama Biochem J 373, 451 (2003)
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Pathway Mathematical ModelPathway Mathematical Model
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Materi & Wishart Drug Discov Today 12, 295 (2007)
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Pathway Mathematical ModelPathway Mathematical Model
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Hatakeyama Biochem J 373, 451 (2003)
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Pathway Simulation EquationsPathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)
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Pathway Pathway Simulation Simulation EquationsEquations
Hatakeyama Biochem J 373, 451 (2003)
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Pathway Simulation EquationsPathway Simulation Equations
Hatakeyama Biochem J 373, 451 (2003)
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Pathway Simulation ParametersPathway Simulation ParametersHatakeyama Biochem J 373, 451
(2003)
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Pathway Simulation ParametersPathway Simulation Parameters
Hatakeyama Biochem J 373, 451 (2003)
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Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein PairsExploration of Similarity Protein Pairs
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Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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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)
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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)
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Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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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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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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Pathway Simulation Parameter Estimation I: Pathway Simulation Parameter Estimation I: Exploration of Similarity Protein Pairs Exploration of Similarity Protein Pairs
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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)
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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)
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)
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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)
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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)
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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)
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
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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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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)
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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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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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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: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)
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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)
BMC Bioinformatics 8, 373 (2007)
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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)
BMC Bioinformatics 8, 373 (2007)
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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)
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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