Numerical Computer Methods, Part D

Erscheinungsjahr 2004
ISBN: 978-0-12-182788-5
Verlag: William Andrew Publishing

Buch, Englisch, 489 Seiten, Format (B × H): 152 mm x 229 mm, Gewicht: 860 g

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.

Zielgruppe

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

Autoren/Hrsg.

Weitere Mitwirkende

Brand, Ludwig

Johnson, Michael L.

Fachgebiete

• Naturwissenschaften Biowissenschaften Enzymologie
• Naturwissenschaften Physik Angewandte Physik Biophysik
• Naturwissenschaften Biowissenschaften Angewandte Biologie Biophysik

Inhaltsverzeichnis

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

Conc

Über Autor(innen)

Edited by Ludwig Brand and Michael L. Johnson