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1.

電子ブック

EB
Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , 2009
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目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1:
Introduction
Estimation of Phase Response Curves / 2:
Specific Applications / 3:
Discussion / 4:
Acknowledgments / Appendix I:
References
Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard
Biochemical Conventions and Calculations
Application to Physiological Systems
Acknowledgment
Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke
Decomposition of Sensor Errors
Measures of Average Glycemia and Deviation from Target
Risk and Variability Assessment
Measures and Plots of System Stability / 5:
Time-Series-Based Prediction of Future BG Values / 6:
Conclusions / 7:
Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger
Methodology
Job Submission
Results
Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels
The Chemical Master Equation
The Stochastic Simulation Algorithm
The Tau-Leaping Method
Measurement of Simulation Error
Software and Two Numerical Experiments
Conclusion
Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse
Types of Biological Data and Their Acquisition
Analysis in the Time Domain
Analysis in the Frequency Domain
Time/Frequency Analysis and the Wavelet Transform
Signal Conditioning
Strength and Regularity of a Signal
A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8:
Computational Design of Surface Charge-Charge Interactions
Experimental Verification of Computational Predictions
Closing Remarks
Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen
Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region
Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces
Locating the Boundary of the Smallest Multidimensional Confidence Region
Finding the Minimum and Maximum of the Prediction Model over the Confidence Region
An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation
95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation
Appendix
Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9:
Calculating the pH Dependence of Protein Characteristics
Setting up and Running a pKa/ Calculation
Analyzing the Results of a pKa/ Calculation
How Reliable Are Calculated pKa/ Values?
Predicting pH Activity Profiles
Decomposition Analysis
Predicting Protein Stability Profiles
Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles
Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10:
Review of Least Squares
Experiment Design Using Vprior/-Numerical Illustrations
Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11:
Conceptual Overview of Model Evaluation and Comparison
Model Comparison Methods
Model Comparison at Work: Choosing between Protein Folding Models
Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12:
Course Description
Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13:
Extracting Melting Curves from Raw Fluorescence
Methods Used for Clustering and Classifying Melting Curves by Genotype
Methods Used for Modeling Melting Curves
Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14:
Early Attempts to Identify and Characterize Pulsatile Hormone Release
Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection
Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts
Limitations and Subsequent Improvements in Deconvolution Procedures
Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model
Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy
Evaluation of Coupled Systems
Evaluation of Hormonal Networks with Feedback Interactions
Future Directions
AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15:
Methods
Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16:
Author Index
Subject Index
Contributors
Preface
Volumes in Series
2.

電子ブック

EB
Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , 2009
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics / Jad Walters ; Sara L. Milam ; A. Clay Clark1:
Introduction
Equilibrium Unfolding / 2:
Measuring Folding Kinetics / 3:
References
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory / Keith D. Connaghan-Jones ; David L. Bain
Assessing Protein Functional and Structural Homogeneity
Dissecting Linked Assembly Reactions
Analysis and Dissection of Natural Promoters / 4:
Measuring the Energetics of Coactivator Recruitment / 5:
Correlation to Biological Function / 6:
Conclusions and Future Directions / 7:
Acknowledgments
General Principles / Dan Grilley ; Ana Maria Soto ; David E. Draper
Ion-Binding Properties of HQS
Preparation of Solutions and Reagents
Instrumentation and Data Collection Protocols
Data Analysis
Controls and Further Considerations
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models / Tural Aksel ; Doug Barrick
Historical Overview of Ising Models and Motivation for the Present Review
Linear Repeat Proteins and Their Connection to Linear Ising Models
Formulating a Homopolymer Partition Function and the Zipper Approximation
Matrix Approach: Homopolymers
Matrix Approach: Heteropolymers
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding
Matrix Homopolymer Analysis of Consensus TPR Folding
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding / 8:
Summary and Future Directions / 9:
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials / Ernesto Freire ; Arne Schön ; Adrian Velazquez-Campoy
The Binding Polynomial
Microscopic Constants and Cooperativity
Independent or Cooperative Binding?
Analysis of ITC Data Using Binding Polynomials
A Typical Case: Macromolecule with Two Ligand-Binding Sites
Data Interpretation
An Experimental Example
Experimental Situations from the Literature / 10:
Macromolecule with Three Ligand-Binding Sites / 11:
Conclusions / 12:
Appendix
Acknowledgment
Kinetic and Equilibrium Analysis of the Myosin ATPase / Enrique M. De La Cruz ; E. Michael Ostap
Reagents and Equipment Used for all Assays
Steady-State ATPase Activity of Myosin
Steady-State Measurement of Actomyosin Binding Affinities
Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions
Kinetic Simulations
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin / Jo M. Holt ; Gary K. Ackers
Cooperativity and Intrinsic Binding
The Macroscopic Binding Isotherm
The Hill Coefficient
Microscopic Cooperativity in Hemoglobin
Summary
Methods for Measuring the Thermodynamic Stability of Membrane Proteins / Heedeok Hong ; Nathan H. Joh ; James U. Bowie ; Lukas K. Tamm
Two Classes of Membrane Proteins
Methods for Measuring Transmembrane Domain Oligomer Stability
Methods for Measuring Multipass ?-helical Membrane Protein Stability
Methods to Study the Stability of ?-barrel Membrane Proteins
A Few Salient Results on Forces that Stabilize Membrane Proteins
Conclusion and Outlook
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands / Gregory Benison ; Elisar Barbar
NMR Methodology
Monomer-dimer Equilibrium Coupled to Electrostatics
Dimerization is Coupled to Ligand Binding
Folding is Coupled to Binding
Allostery in LC8
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry / Michael T. Henzl
Practical Aspects of Data Collection
Illustrative Global ITC Analyses of Divalent Ion Binding
Conclusion
Energetic Profiling of Protein Folds / Jason Vertrees ; James O. Wrabl ; Vincent J. Hilser
Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics
Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble
Principal Components Analysis of Energetic Profile Space
Energetic Profiles are Conserved Between Homologous Proteins
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm
CE Algorithm Described for Structure Coordinates
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation / Juyang Huang
Materials and Methods
Result and Discussion
Concluding Remarks
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding / Nathan A. Siegfried ; Philip C. Bevilacqua13:
Folding Cooperativity Defined
Thermodynamic Boxes: Design, Implementation, and Interpretation
Thermodynamic Cubes: Design, Implementation, and Interpretation
Examples of Cooperativity in RNA
Measuring Thermodynamic Parameters by UV Melting
The Thermodynamics of Virus Capsid Assembly / Sarah Katen ; Adam Zlotnick14:
The Structural Basis of Capsid Stability
Analysis of Capsid Stability
Applications of Thermodynamic Evaluation of Virus Capsid Stability
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems / John J. Correia ; Walter F. Stafford15:
Methods
Simulation and Analysis of Dimerization
Kinetically Mediated Dimerization
A Stepwise Approach
Final Thoughts
Author Index
Subject Index
Contributors
Preface
Volumes in Series
3.

電子ブック

EB
Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Elsevier Science & Technology, 2009
所蔵情報: loading…
目次情報: 続きを見る
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried4:
Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton5:
Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner6:
Metadynamics methods applied to ion channel gating / Carmen Domene7:
Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov8:
Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad9:
Energetics of the collagen triple helix / Yujia Xu10:
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze11:
Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger12:
Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu13:
Energetic methods applied to allostery in thrombin / Enrico Di Cera14:
Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov15:
Solvent denaturation of proteins and the interpretation of the m-value / J. Martin Scholtz ; Nick Pace16:
Energetic approaches to the characterization of the E. coli PriA helicase / Wlodek Bujalowski17:
Protein-protein interactions and macromolecular stability / Lisa Gloss18:
Methods for assessing T cell receptor recognition / Brian M Baker19:
Thermodynamic analysis applied to bromodomain-histone interactions / Martin Thompson20:
Thermodynamic parameters fo dimer-dimer interaction in 2-cys peroxiredoxin / Karl-Josef Dietz21:
Small molecule-membrane interactions / Anne Hinderliter22:
Constant pH molecular dynamics simulations / Jana Khandogin Shen23:
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
4.

電子ブック

EB
Michael L. John, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Elsevier Science & Technology, 2009
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram1:
Introduction
Scatter Plots and Correlation Analysis / 2:
Example 1: Relaxation Oscillations / 3:
Example 2: Square Wave Bursting / 4:
Example 3: Elliptic Bursting / 5:
Example 4: Using Correlation Analysis on Experimental Data / 6:
Summary / 7:
Acknowledgments
References
Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu
Background
Experimental and Computational Workflow
Application to Traits Relevant to Cancer Progression
Conclusions
Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs
Overview of Methods
Application to the Rosetta Compendium
Results of Analyses
Discussion
Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee
Mathematical Modeling of the Immune Network
Two Examples of Models to Understand T Cell Regulation
How to Implement Mathematical Models in Computer Simulations
Concluding Remarks
Acknowledgmentss
Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian
Energy
Entropy and ôThermoö-dynamics of Markov Processes
A Three-State Two-Cycle Motor Protein
Phosphorylation-Dephosphorylation Cycle1 Kinetics
Summary and Challenges
Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford
Methods
ABCD Systems
Monomer-Tetramer Model
Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah
Computational Systems Biology
Network Inference
Reverse-Engineering of Discrete Models: An Example
High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw8:
What is an HTC Application?
HTC Technologies
High-Throughput Computing Examples
Advanced Topics
Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert9:
Systems and Data Sources
Data Integration
Artificial Neural Network Training and Validation
Future Development and Enhancement Plans
DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ10:
Equilibrium Binding Studies
Initial Rates of Enzyme Reactions
Time Course of Enzyme Reactions
General Methods and Algorithms
Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang11:
Cellular Signaling Networks
Boolean Dynamic Modeling
Variants of Boolean Network Models
Application Examples
Conclusion and Discussion
The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept12:
Homology Modeling
Molecular Dynamics
Molecular Docking
Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison13:
Boolean Networks
Differential Equation Models
Probabilistic Boolean Networks
Stochastic Differential Equation Models
Bayesian Probability Approach to ADHD Appraisal / Raina Robeva ; Jennifer Kim Penberthy14:
Bayesian Probability Algorithm
The Value of Bayesian Probability Approach as a Meta-Analysis Tool
Discussion and Future Directions
Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin15:
Understanding Reaction Dynamics
Graphical Notation
Reactions
Reaction Kinetics
Transition Firing Rules
Notes
Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns16:
Modeling Approach
Methods for Simulation Study
Results
Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17:
Hypothalamic-Pituitary-Adrenal Axis System
Development of a Clinically Relevant Performance-Assessment Tools
Dynamic Programming
Computation of Optimal Treatments for HPA Axis System
Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18:
Molecular-Level Kinetics Models: Simulation of In Vitro Experiments
Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions
Single-Tissue Compartmental Models: Simulation at In Vivo Tissue
Multitissue Compartmental Models: Simulation of Whole Body
The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / Joel Tellinghuisen19:
Least Squares Review
Statistics of Reciprocals
Weights When y is a True Dependent Variable
Unusual Weighting: When x is the Dependent Variable
Assessing Data Uncertainty: Variance Function Estimation
Conclusion
Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20:
Motivating Application: Classifying Cardiac Rhythms
Renyi Entropy and the Friedman-Tukey Index
Kernel Density Estimation
Mean-Integrated Square Error
Estimating the FT Index
Connection Between Template Matches and Kernel Densities
Summary and Future Work
Pancreatic Network Control of Glucagon Secretion and Counterregulation / Leon S. Farhy ; Anthony L. McCall21:
Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes
Interdisciplinary Approach to Investigating the Defects in the GCR
Initial Qualitative Analysis of the GCR Control Axis
Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats
Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas
Advantages and Limitations of the Interdisciplinary Approach
Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22:
Computational Modeling and Enzyme Kinetics
Yeast Triosephosphate Isomerase (EC 5.3.1.1)
Initial Rate Analysis
Progress Curve Analysis
Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23:
Challenges of Fitting by Simulation
Progress Curve Kinetics
Fitting Full Progress Curves
Slow Onset Inhibition Kinetics
Author Index
Subject Index
Contributors
Preface
Volumes in Series
5.

電子ブック

EB
Ludwig; Johnson, Michael L.; Brand, Ludwig Brand, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1:
Introduction
Estimation of Phase Response Curves / 2:
Specific Applications / 3:
Discussion / 4:
Acknowledgments / Appendix I:
References
Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard
Biochemical Conventions and Calculations
Application to Physiological Systems
Acknowledgment
Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke
Decomposition of Sensor Errors
Measures of Average Glycemia and Deviation from Target
Risk and Variability Assessment
Measures and Plots of System Stability / 5:
Time-Series-Based Prediction of Future BG Values / 6:
Conclusions / 7:
Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger
Methodology
Job Submission
Results
Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels
The Chemical Master Equation
The Stochastic Simulation Algorithm
The Tau-Leaping Method
Measurement of Simulation Error
Software and Two Numerical Experiments
Conclusion
Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse
Types of Biological Data and Their Acquisition
Analysis in the Time Domain
Analysis in the Frequency Domain
Time/Frequency Analysis and the Wavelet Transform
Signal Conditioning
Strength and Regularity of a Signal
A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8:
Computational Design of Surface Charge-Charge Interactions
Experimental Verification of Computational Predictions
Closing Remarks
Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen
Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region
Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces
Locating the Boundary of the Smallest Multidimensional Confidence Region
Finding the Minimum and Maximum of the Prediction Model over the Confidence Region
An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation
95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation
Appendix
Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9:
Calculating the pH Dependence of Protein Characteristics
Setting up and Running a pKa/ Calculation
Analyzing the Results of a pKa/ Calculation
How Reliable Are Calculated pKa/ Values?
Predicting pH Activity Profiles
Decomposition Analysis
Predicting Protein Stability Profiles
Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles
Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10:
Review of Least Squares
Experiment Design Using Vprior/-Numerical Illustrations
Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11:
Conceptual Overview of Model Evaluation and Comparison
Model Comparison Methods
Model Comparison at Work: Choosing between Protein Folding Models
Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12:
Course Description
Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13:
Extracting Melting Curves from Raw Fluorescence
Methods Used for Clustering and Classifying Melting Curves by Genotype
Methods Used for Modeling Melting Curves
Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14:
Early Attempts to Identify and Characterize Pulsatile Hormone Release
Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection
Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts
Limitations and Subsequent Improvements in Deconvolution Procedures
Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model
Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy
Evaluation of Coupled Systems
Evaluation of Hormonal Networks with Feedback Interactions
Future Directions
AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15:
Methods
Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16:
Author Index
Subject Index
Contributors
Preface
Volumes in Series
6.

電子ブック

EB
Michael L.; Holt, Jo M.; Ackers, Gary K.; Johnson, Michael L Johnson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics / Jad Walters ; Sara L. Milam ; A. Clay Clark1:
Introduction
Equilibrium Unfolding / 2:
Measuring Folding Kinetics / 3:
References
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory / Keith D. Connaghan-Jones ; David L. Bain
Assessing Protein Functional and Structural Homogeneity
Dissecting Linked Assembly Reactions
Analysis and Dissection of Natural Promoters / 4:
Measuring the Energetics of Coactivator Recruitment / 5:
Correlation to Biological Function / 6:
Conclusions and Future Directions / 7:
Acknowledgments
General Principles / Dan Grilley ; Ana Maria Soto ; David E. Draper
Ion-Binding Properties of HQS
Preparation of Solutions and Reagents
Instrumentation and Data Collection Protocols
Data Analysis
Controls and Further Considerations
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models / Tural Aksel ; Doug Barrick
Historical Overview of Ising Models and Motivation for the Present Review
Linear Repeat Proteins and Their Connection to Linear Ising Models
Formulating a Homopolymer Partition Function and the Zipper Approximation
Matrix Approach: Homopolymers
Matrix Approach: Heteropolymers
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding
Matrix Homopolymer Analysis of Consensus TPR Folding
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding / 8:
Summary and Future Directions / 9:
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials / Ernesto Freire ; Arne Schön ; Adrian Velazquez-Campoy
The Binding Polynomial
Microscopic Constants and Cooperativity
Independent or Cooperative Binding?
Analysis of ITC Data Using Binding Polynomials
A Typical Case: Macromolecule with Two Ligand-Binding Sites
Data Interpretation
An Experimental Example
Experimental Situations from the Literature / 10:
Macromolecule with Three Ligand-Binding Sites / 11:
Conclusions / 12:
Appendix
Acknowledgment
Kinetic and Equilibrium Analysis of the Myosin ATPase / Enrique M. De La Cruz ; E. Michael Ostap
Reagents and Equipment Used for all Assays
Steady-State ATPase Activity of Myosin
Steady-State Measurement of Actomyosin Binding Affinities
Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions
Kinetic Simulations
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin / Jo M. Holt ; Gary K. Ackers
Cooperativity and Intrinsic Binding
The Macroscopic Binding Isotherm
The Hill Coefficient
Microscopic Cooperativity in Hemoglobin
Summary
Methods for Measuring the Thermodynamic Stability of Membrane Proteins / Heedeok Hong ; Nathan H. Joh ; James U. Bowie ; Lukas K. Tamm
Two Classes of Membrane Proteins
Methods for Measuring Transmembrane Domain Oligomer Stability
Methods for Measuring Multipass ?-helical Membrane Protein Stability
Methods to Study the Stability of ?-barrel Membrane Proteins
A Few Salient Results on Forces that Stabilize Membrane Proteins
Conclusion and Outlook
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands / Gregory Benison ; Elisar Barbar
NMR Methodology
Monomer-dimer Equilibrium Coupled to Electrostatics
Dimerization is Coupled to Ligand Binding
Folding is Coupled to Binding
Allostery in LC8
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry / Michael T. Henzl
Practical Aspects of Data Collection
Illustrative Global ITC Analyses of Divalent Ion Binding
Conclusion
Energetic Profiling of Protein Folds / Jason Vertrees ; James O. Wrabl ; Vincent J. Hilser
Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics
Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble
Principal Components Analysis of Energetic Profile Space
Energetic Profiles are Conserved Between Homologous Proteins
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm
CE Algorithm Described for Structure Coordinates
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation / Juyang Huang
Materials and Methods
Result and Discussion
Concluding Remarks
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding / Nathan A. Siegfried ; Philip C. Bevilacqua13:
Folding Cooperativity Defined
Thermodynamic Boxes: Design, Implementation, and Interpretation
Thermodynamic Cubes: Design, Implementation, and Interpretation
Examples of Cooperativity in RNA
Measuring Thermodynamic Parameters by UV Melting
The Thermodynamics of Virus Capsid Assembly / Sarah Katen ; Adam Zlotnick14:
The Structural Basis of Capsid Stability
Analysis of Capsid Stability
Applications of Thermodynamic Evaluation of Virus Capsid Stability
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems / John J. Correia ; Walter F. Stafford15:
Methods
Simulation and Analysis of Dimerization
Kinetically Mediated Dimerization
A Stepwise Approach
Final Thoughts
Author Index
Subject Index
Contributors
Preface
Volumes in Series
7.

電子ブック

EB
Michael L.; Holt, Jo M.; Ackers, Gary K.; Ackers, Gary K Johnson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
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NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried4:
Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton5:
Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner6:
Metadynamics methods applied to ion channel gating / Carmen Domene7:
Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov8:
Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad9:
Energetics of the collagen triple helix / Yujia Xu10:
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze11:
Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger12:
Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu13:
Energetic methods applied to allostery in thrombin / Enrico Di Cera14:
Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov15:
Solvent denaturation of proteins and the interpretation of the m-value / J. Martin Scholtz ; Nick Pace16:
Energetic approaches to the characterization of the E. coli PriA helicase / Wlodek Bujalowski17:
Protein-protein interactions and macromolecular stability / Lisa Gloss18:
Methods for assessing T cell receptor recognition / Brian M Baker19:
Thermodynamic analysis applied to bromodomain-histone interactions / Martin Thompson20:
Thermodynamic parameters fo dimer-dimer interaction in 2-cys peroxiredoxin / Karl-Josef Dietz21:
Small molecule-membrane interactions / Anne Hinderliter22:
Constant pH molecular dynamics simulations / Jana Khandogin Shen23:
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
8.

電子ブック

EB
Michael L. John, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
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Contributors
Preface
Volumes in Series
Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram1:
Introduction
Scatter Plots and Correlation Analysis / 2:
Example 1: Relaxation Oscillations / 3:
Example 2: Square Wave Bursting / 4:
Example 3: Elliptic Bursting / 5:
Example 4: Using Correlation Analysis on Experimental Data / 6:
Summary / 7:
Acknowledgments
References
Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu
Background
Experimental and Computational Workflow
Application to Traits Relevant to Cancer Progression
Conclusions
Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs
Overview of Methods
Application to the Rosetta Compendium
Results of Analyses
Discussion
Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee
Mathematical Modeling of the Immune Network
Two Examples of Models to Understand T Cell Regulation
How to Implement Mathematical Models in Computer Simulations
Concluding Remarks
Acknowledgmentss
Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian
Energy
Entropy and ôThermoö-dynamics of Markov Processes
A Three-State Two-Cycle Motor Protein
Phosphorylation-Dephosphorylation Cycle1 Kinetics
Summary and Challenges
Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford
Methods
ABCD Systems
Monomer-Tetramer Model
Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah
Computational Systems Biology
Network Inference
Reverse-Engineering of Discrete Models: An Example
High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw8:
What is an HTC Application?
HTC Technologies
High-Throughput Computing Examples
Advanced Topics
Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert9:
Systems and Data Sources
Data Integration
Artificial Neural Network Training and Validation
Future Development and Enhancement Plans
DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ10:
Equilibrium Binding Studies
Initial Rates of Enzyme Reactions
Time Course of Enzyme Reactions
General Methods and Algorithms
Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang11:
Cellular Signaling Networks
Boolean Dynamic Modeling
Variants of Boolean Network Models
Application Examples
Conclusion and Discussion
The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept12:
Homology Modeling
Molecular Dynamics
Molecular Docking
Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison13:
Boolean Networks
Differential Equation Models
Probabilistic Boolean Networks
Stochastic Differential Equation Models
Bayesian Probability Approach to ADHD Appraisal / Raina Robeva ; Jennifer Kim Penberthy14:
Bayesian Probability Algorithm
The Value of Bayesian Probability Approach as a Meta-Analysis Tool
Discussion and Future Directions
Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin15:
Understanding Reaction Dynamics
Graphical Notation
Reactions
Reaction Kinetics
Transition Firing Rules
Notes
Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns16:
Modeling Approach
Methods for Simulation Study
Results
Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17:
Hypothalamic-Pituitary-Adrenal Axis System
Development of a Clinically Relevant Performance-Assessment Tools
Dynamic Programming
Computation of Optimal Treatments for HPA Axis System
Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18:
Molecular-Level Kinetics Models: Simulation of In Vitro Experiments
Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions
Single-Tissue Compartmental Models: Simulation at In Vivo Tissue
Multitissue Compartmental Models: Simulation of Whole Body
The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / Joel Tellinghuisen19:
Least Squares Review
Statistics of Reciprocals
Weights When y is a True Dependent Variable
Unusual Weighting: When x is the Dependent Variable
Assessing Data Uncertainty: Variance Function Estimation
Conclusion
Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20:
Motivating Application: Classifying Cardiac Rhythms
Renyi Entropy and the Friedman-Tukey Index
Kernel Density Estimation
Mean-Integrated Square Error
Estimating the FT Index
Connection Between Template Matches and Kernel Densities
Summary and Future Work
Pancreatic Network Control of Glucagon Secretion and Counterregulation / Leon S. Farhy ; Anthony L. McCall21:
Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes
Interdisciplinary Approach to Investigating the Defects in the GCR
Initial Qualitative Analysis of the GCR Control Axis
Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats
Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas
Advantages and Limitations of the Interdisciplinary Approach
Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22:
Computational Modeling and Enzyme Kinetics
Yeast Triosephosphate Isomerase (EC 5.3.1.1)
Initial Rate Analysis
Progress Curve Analysis
Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23:
Challenges of Fitting by Simulation
Progress Curve Kinetics
Fitting Full Progress Curves
Slow Onset Inhibition Kinetics
Author Index
Subject Index
Contributors
Preface
Volumes in Series
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