AUTUMN SALE
Fall into wisdom!
Save up to 20% on books and eBooks. Free shipping. No promo code needed.
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 concom… Read more
AUTUMN SALE
Save up to 20% on books and eBooks. Free shipping. No promo code needed.
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 ΔH° 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
Appendix I: Outline of Proof of Proposition 1
Appendix II: Proof of Lemma 1
Appendix III: Proof of Lemma 2
Bayesian Methods to Improve Sample Size Approximations
Introduction
Bayesian Inference
Deriving Sample Size Formulas
Choosing Prior Distributions
Gain from Using Prior Information
Examples
Conclusion
Distribution Functions from Moments and the Maximum-Entropy Method
Introduction
Ligand Binding: Moments
Maximum-Entropy Distributions
Ligand Binding: Distribution Functions
Enthalpy Distributions
Self-Association Distributions
Author Index
Subject Index
LB
MJ