Ludwig Brand / Michael L. Johnson (eds.)
Numerical Computer Methods, Part D
Volume 383
Herausgegeben:Brand, Ludwig; Johnson, Michael L.
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Ludwig Brand / Michael L. Johnson (eds.)
Numerical Computer Methods, Part D
Volume 383
Herausgegeben:Brand, Ludwig; Johnson, Michael L.
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The aim of Numerical Computer Methods, Part D is to brief researchers of the importance of data analysis in enzymology, and of the modern methods that have developed concomitantly with computer hardware. It is also to validate researchers' computer programs with real and synthetic data to ascertain that the results produced are what they expected.
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The aim of Numerical Computer Methods, Part D is to brief researchers of the importance of data analysis in enzymology, and of the modern methods that have developed concomitantly with computer hardware. It is also to validate researchers' computer programs with real and synthetic data to ascertain that the results produced are what they expected.
Produktdetails
- Produktdetails
- Methods in Enzymology Volume 383
- Verlag: Academic Press / Elsevier Science & Technology
- Artikelnr. des Verlages: S0076-6879(00)X0384-9
- Seitenzahl: 489
- Erscheinungstermin: 26. März 2004
- Englisch
- Abmessung: 234mm x 164mm x 25mm
- Gewicht: 972g
- ISBN-13: 9780121827885
- ISBN-10: 0121827887
- Artikelnr.: 21288701
- Methods in Enzymology Volume 383
- Verlag: Academic Press / Elsevier Science & Technology
- Artikelnr. des Verlages: S0076-6879(00)X0384-9
- Seitenzahl: 489
- Erscheinungstermin: 26. März 2004
- Englisch
- Abmessung: 234mm x 164mm x 25mm
- Gewicht: 972g
- ISBN-13: 9780121827885
- ISBN-10: 0121827887
- Artikelnr.: 21288701
Editors-In-Chief
Contributors to Volume 383
Preface
Methods In Enzymology
Prediction of Protein Structure
Overview and Perspective
Classifications of Protein Structure
Concepts and Evaluations of Protein Predictions
Process of Extracting Information about Protein Structure from Sequence
Future Directions
Modeling and Studying Proteins with Molecular Dynamics
Introduction
Sampling of CHARMM Capabilities
Program Operation Basics
Example Analysis
Ab Initio Protein Folding Using LINUS
Introduction
Anatomy of LINUS Simulation
Implementation
Simulation Examples
Conclusion
Appendix I
Protein Structure Prediction Using Rosetta
Introduction
Rosetta Strategy
De Novo Structure Prediction with Rosetta
Structure Prediction by Fragment Assembly
Enhancements of Fragment Insertion Strategy
Effectiveness of Conformation Modification Operators for Energy Function Optimization
Conclusions
Supplemental Materials
Appendix I
Appendix II
Poisson-Boltzmann Methods for Biomolecular Electrostatics
Introduction
Numerical Solution of Poisson-Boltzmann Equation
Applications to Biomedical Sciences
Conclusions
Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
Introduction
Replica Exchange Molecular Dynamics
Practical Issues
Appendix
DNA Microarray Time Series Analysis: Automated Statistical Assessment of Circadian Rhythms in Gene Expression Patterning
Introduction
Statistical Assessment of Daily Rhythms in Microarray Data
Simulation Procedure
Comparisons of Analytical Results
Summary
Molecular Simulations of Diffusion and Association in Multimacromolecular Systems
Introduction
Theoretical Aspects
Practical Aspects
Some Example Applications
Conclusion
Modeling Lipid-Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and Rafts
Introduction
Theoretical Models
Simulation Methods
Results
Summary and Perspectives
Idealization and Simulation of Single Ion Channel Data
Introduction
Noise
Filtering
Missed Events
Subconductance Levels
Models
Analysis Methods
Simulation
Idealization
Interpretation
Performance
Statistical Error in Isothermal Titration Calorimetry
Introduction
Variance-Covariance Matrix in Least Squares
Monte Carlo Computational Methods
Van't Hoff Analysis of K°(T): Least-Squares Demonstration
Isothermal Titration Calorimetry
Calorimetric Versus Van't Hoff DeltaH° from ITC
Conclusion
Analysis of Circular Dichroism Data
Introduction
Summary of Methods to Obtain Secondary Structure of Proteins from Circular Dichroism Data
Determination of Thermodynamics of Protein Folding/Unfolding from CD Data
Determination of Binding Constants from CD Data
Conclusion
Appendix I
Computation and Analysis of Protein Circular Dichroism Spectra
Introduction
Basic Definitions
Computation of Protein CD
Analysis of Protein CD
Model Comparison Methods
Introduction
Statistical Foundations of Model Comparison
Model Comparison Methods
Model Comparison at Work
Conclusion
Practical Robust Fit of Enzyme Inhibition Data
Introduction
Theory
Numerical Example
Implementation Notes
Conclusions
Measuring Period of Human Biological Clock: Infill Asymptotic Analysis of Harmonic Regression Parameter Estimates
Introduction
Theory
Proof
Proof
Proof
Data Analysis
Discussion<
Contributors to Volume 383
Preface
Methods In Enzymology
Prediction of Protein Structure
Overview and Perspective
Classifications of Protein Structure
Concepts and Evaluations of Protein Predictions
Process of Extracting Information about Protein Structure from Sequence
Future Directions
Modeling and Studying Proteins with Molecular Dynamics
Introduction
Sampling of CHARMM Capabilities
Program Operation Basics
Example Analysis
Ab Initio Protein Folding Using LINUS
Introduction
Anatomy of LINUS Simulation
Implementation
Simulation Examples
Conclusion
Appendix I
Protein Structure Prediction Using Rosetta
Introduction
Rosetta Strategy
De Novo Structure Prediction with Rosetta
Structure Prediction by Fragment Assembly
Enhancements of Fragment Insertion Strategy
Effectiveness of Conformation Modification Operators for Energy Function Optimization
Conclusions
Supplemental Materials
Appendix I
Appendix II
Poisson-Boltzmann Methods for Biomolecular Electrostatics
Introduction
Numerical Solution of Poisson-Boltzmann Equation
Applications to Biomedical Sciences
Conclusions
Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
Introduction
Replica Exchange Molecular Dynamics
Practical Issues
Appendix
DNA Microarray Time Series Analysis: Automated Statistical Assessment of Circadian Rhythms in Gene Expression Patterning
Introduction
Statistical Assessment of Daily Rhythms in Microarray Data
Simulation Procedure
Comparisons of Analytical Results
Summary
Molecular Simulations of Diffusion and Association in Multimacromolecular Systems
Introduction
Theoretical Aspects
Practical Aspects
Some Example Applications
Conclusion
Modeling Lipid-Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and Rafts
Introduction
Theoretical Models
Simulation Methods
Results
Summary and Perspectives
Idealization and Simulation of Single Ion Channel Data
Introduction
Noise
Filtering
Missed Events
Subconductance Levels
Models
Analysis Methods
Simulation
Idealization
Interpretation
Performance
Statistical Error in Isothermal Titration Calorimetry
Introduction
Variance-Covariance Matrix in Least Squares
Monte Carlo Computational Methods
Van't Hoff Analysis of K°(T): Least-Squares Demonstration
Isothermal Titration Calorimetry
Calorimetric Versus Van't Hoff DeltaH° from ITC
Conclusion
Analysis of Circular Dichroism Data
Introduction
Summary of Methods to Obtain Secondary Structure of Proteins from Circular Dichroism Data
Determination of Thermodynamics of Protein Folding/Unfolding from CD Data
Determination of Binding Constants from CD Data
Conclusion
Appendix I
Computation and Analysis of Protein Circular Dichroism Spectra
Introduction
Basic Definitions
Computation of Protein CD
Analysis of Protein CD
Model Comparison Methods
Introduction
Statistical Foundations of Model Comparison
Model Comparison Methods
Model Comparison at Work
Conclusion
Practical Robust Fit of Enzyme Inhibition Data
Introduction
Theory
Numerical Example
Implementation Notes
Conclusions
Measuring Period of Human Biological Clock: Infill Asymptotic Analysis of Harmonic Regression Parameter Estimates
Introduction
Theory
Proof
Proof
Proof
Data Analysis
Discussion<
Editors-In-Chief
Contributors to Volume 383
Preface
Methods In Enzymology
Prediction of Protein Structure
Overview and Perspective
Classifications of Protein Structure
Concepts and Evaluations of Protein Predictions
Process of Extracting Information about Protein Structure from Sequence
Future Directions
Modeling and Studying Proteins with Molecular Dynamics
Introduction
Sampling of CHARMM Capabilities
Program Operation Basics
Example Analysis
Ab Initio Protein Folding Using LINUS
Introduction
Anatomy of LINUS Simulation
Implementation
Simulation Examples
Conclusion
Appendix I
Protein Structure Prediction Using Rosetta
Introduction
Rosetta Strategy
De Novo Structure Prediction with Rosetta
Structure Prediction by Fragment Assembly
Enhancements of Fragment Insertion Strategy
Effectiveness of Conformation Modification Operators for Energy Function Optimization
Conclusions
Supplemental Materials
Appendix I
Appendix II
Poisson-Boltzmann Methods for Biomolecular Electrostatics
Introduction
Numerical Solution of Poisson-Boltzmann Equation
Applications to Biomedical Sciences
Conclusions
Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
Introduction
Replica Exchange Molecular Dynamics
Practical Issues
Appendix
DNA Microarray Time Series Analysis: Automated Statistical Assessment of Circadian Rhythms in Gene Expression Patterning
Introduction
Statistical Assessment of Daily Rhythms in Microarray Data
Simulation Procedure
Comparisons of Analytical Results
Summary
Molecular Simulations of Diffusion and Association in Multimacromolecular Systems
Introduction
Theoretical Aspects
Practical Aspects
Some Example Applications
Conclusion
Modeling Lipid-Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and Rafts
Introduction
Theoretical Models
Simulation Methods
Results
Summary and Perspectives
Idealization and Simulation of Single Ion Channel Data
Introduction
Noise
Filtering
Missed Events
Subconductance Levels
Models
Analysis Methods
Simulation
Idealization
Interpretation
Performance
Statistical Error in Isothermal Titration Calorimetry
Introduction
Variance-Covariance Matrix in Least Squares
Monte Carlo Computational Methods
Van't Hoff Analysis of K°(T): Least-Squares Demonstration
Isothermal Titration Calorimetry
Calorimetric Versus Van't Hoff DeltaH° from ITC
Conclusion
Analysis of Circular Dichroism Data
Introduction
Summary of Methods to Obtain Secondary Structure of Proteins from Circular Dichroism Data
Determination of Thermodynamics of Protein Folding/Unfolding from CD Data
Determination of Binding Constants from CD Data
Conclusion
Appendix I
Computation and Analysis of Protein Circular Dichroism Spectra
Introduction
Basic Definitions
Computation of Protein CD
Analysis of Protein CD
Model Comparison Methods
Introduction
Statistical Foundations of Model Comparison
Model Comparison Methods
Model Comparison at Work
Conclusion
Practical Robust Fit of Enzyme Inhibition Data
Introduction
Theory
Numerical Example
Implementation Notes
Conclusions
Measuring Period of Human Biological Clock: Infill Asymptotic Analysis of Harmonic Regression Parameter Estimates
Introduction
Theory
Proof
Proof
Proof
Data Analysis
Discussion<
Contributors to Volume 383
Preface
Methods In Enzymology
Prediction of Protein Structure
Overview and Perspective
Classifications of Protein Structure
Concepts and Evaluations of Protein Predictions
Process of Extracting Information about Protein Structure from Sequence
Future Directions
Modeling and Studying Proteins with Molecular Dynamics
Introduction
Sampling of CHARMM Capabilities
Program Operation Basics
Example Analysis
Ab Initio Protein Folding Using LINUS
Introduction
Anatomy of LINUS Simulation
Implementation
Simulation Examples
Conclusion
Appendix I
Protein Structure Prediction Using Rosetta
Introduction
Rosetta Strategy
De Novo Structure Prediction with Rosetta
Structure Prediction by Fragment Assembly
Enhancements of Fragment Insertion Strategy
Effectiveness of Conformation Modification Operators for Energy Function Optimization
Conclusions
Supplemental Materials
Appendix I
Appendix II
Poisson-Boltzmann Methods for Biomolecular Electrostatics
Introduction
Numerical Solution of Poisson-Boltzmann Equation
Applications to Biomedical Sciences
Conclusions
Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
Introduction
Replica Exchange Molecular Dynamics
Practical Issues
Appendix
DNA Microarray Time Series Analysis: Automated Statistical Assessment of Circadian Rhythms in Gene Expression Patterning
Introduction
Statistical Assessment of Daily Rhythms in Microarray Data
Simulation Procedure
Comparisons of Analytical Results
Summary
Molecular Simulations of Diffusion and Association in Multimacromolecular Systems
Introduction
Theoretical Aspects
Practical Aspects
Some Example Applications
Conclusion
Modeling Lipid-Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and Rafts
Introduction
Theoretical Models
Simulation Methods
Results
Summary and Perspectives
Idealization and Simulation of Single Ion Channel Data
Introduction
Noise
Filtering
Missed Events
Subconductance Levels
Models
Analysis Methods
Simulation
Idealization
Interpretation
Performance
Statistical Error in Isothermal Titration Calorimetry
Introduction
Variance-Covariance Matrix in Least Squares
Monte Carlo Computational Methods
Van't Hoff Analysis of K°(T): Least-Squares Demonstration
Isothermal Titration Calorimetry
Calorimetric Versus Van't Hoff DeltaH° from ITC
Conclusion
Analysis of Circular Dichroism Data
Introduction
Summary of Methods to Obtain Secondary Structure of Proteins from Circular Dichroism Data
Determination of Thermodynamics of Protein Folding/Unfolding from CD Data
Determination of Binding Constants from CD Data
Conclusion
Appendix I
Computation and Analysis of Protein Circular Dichroism Spectra
Introduction
Basic Definitions
Computation of Protein CD
Analysis of Protein CD
Model Comparison Methods
Introduction
Statistical Foundations of Model Comparison
Model Comparison Methods
Model Comparison at Work
Conclusion
Practical Robust Fit of Enzyme Inhibition Data
Introduction
Theory
Numerical Example
Implementation Notes
Conclusions
Measuring Period of Human Biological Clock: Infill Asymptotic Analysis of Harmonic Regression Parameter Estimates
Introduction
Theory
Proof
Proof
Proof
Data Analysis
Discussion<