Numerical Computer Methods, Part D

Numerical Computer Methods, Part D

1st Edition - March 26, 2004
This is the Latest Edition
  • Editors: Ludwig Brand, Michael Johnson
  • eBook ISBN: 9780080497211
  • Hardcover ISBN: 9780121827885

Purchase options

Purchase options
DRM-free (Mobi, PDF, EPub)
Available
Sales tax will be calculated at check-out

Institutional Subscription

Free Global Shipping
No minimum order

Description

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.

Key Features

  • Selected Contents:
    • Prediction of protein structure
    • Modeling and studying proteins with molecular dynamics
    • Statistical error in isothermal titration calorimetry
    • Analysis of circular dichroism data
    • Model comparison methods

Readership

Biochemists, biophysicists, physical chemists, molecular biologists, cell biologists

Table of Contents

  • 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

Product details

  • No. of pages: 489
  • Language: English
  • Copyright: © Academic Press 2004
  • Published: March 26, 2004
  • Imprint: Academic Press
  • eBook ISBN: 9780080497211
  • Hardcover ISBN: 9780121827885

About the Serial Volume Editors

Ludwig Brand

Affiliations and Expertise

McCollum-Pratt Institute, Johns Hopkins University, Baltimore, MD, USA

Michael Johnson

Affiliations and Expertise

University of Virginia Health Sciences Center, Charlottesville, USA