Reviews in Computational Chemistry / Reviews in Computational Chemistry, Volume 22

Name: Reviews in Computational Chemistry / Reviews in Computational Chemistry, Volume 22
Brand: Wiley-VCH
Price: 223.99 EUR
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Kenny B. Lipkowitz Tom Cundari Valerie J. Gillet Donald B. Boyd(Herausgeber*in)

Wiley-VCH (Verlag)

Erschienen am 10. Februar 2006

486 Seiten

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978-0-471-78035-9 (ISBN)

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Inhalt

Intro
Reviews in Computational Chemistry Volume 22
Preface
Contents
Contributors
Contributors to Previous Volumes
1. Protein Structure Classification
Introduction
Classification and Biology
The Biomolecular Revolution
Basic Principles of Protein Structure
Visualization
Protein Building Blocks
Protein Structure Hierarchy
Three Types of Proteins
Geometry of Globular Proteins
Protein Domains
Resources on Protein Structures
Protein Structure Comparison
Automatic Identification of Protein Structural Domains
The Rigid-Body Transformation Problem
Protein Structure Superposition
cRMS: An Ambiguous Measure of Similarity
Differential Geometry and Protein Structure Comparison
Upcoming Challenges for Protein Structure Comparison
Protein Structure Classification
The Structure Classification of Proteins (SCOP)
The CATH Classification
The DALI Domain Dictionary (DDD)
Comparing SCOP, CATH, and DDD
Conclusions
Acknowledgments
Appendix
References
2. Comparative Protein Modeling
Introduction
Anatomy of a Comparative Model
Step 1: Searching for Related Sequences and Structures
Expert Protein Analysis System (ExPASy)
BLAST and PSI-BLAST
Protein Data Bank (PDB)
Sequence Alignment and Modeling System with Hidden Markov Models
Threading
Threader
Example: Finding Related Sequences and 3-D Structures
Step 2: Sequence Alignment
Preparing the Sequences
Alignment Basics
Similarity Matrices
Clustal
Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee)
Divide-and-Conquer Alignment (DCA)
Example: Aligning Sequences
Step 3: Selecting Templates and Improving Alignments
Selecting Templates
Improving Sequence Alignments With Primary and Secondary Structure Analysis
Example: Aligning the Target to the Selected Template
Step 4: Constructing Protein Models
Satisfaction of Spatial Restraints
Segment Match Modeling
Multiple Template Method
3D-JIGSAW
Overall Protein Model Construction Methods
Example: Constructing a Protein Model
Step 5: Refinement of Protein Models
Side-Chains with Rotamer Library (SCWRL)
Energy Minimization
Molecular Dynamics
Molecular Dynamics with Simulated Annealing
Step 6: Evaluating Protein Models
PROCHECK
Verify3D
ERRAT
Protein Structure Analysis (ProSa)
Protein Volume Evaluation (PROVE)
Model Clustering Analysis
Example: Evaluation of Protein Models
Conclusions
References
3. Simulations of Protein Folding
Introduction
Theoretical Framework
Energy Landscape Theory
Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders
Protein Models
Introduction and General Simulation Techniques
Coarse-Grained Protein Models
Fully Atomic Simulations
Advanced Topics: The Transition State Ensemble for Folding
Transition State and Two-State Kinetics
Methods for Identifying the TSE
Conclusions and Future Directions
Acknowledgments
References
4. The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods
Introduction
System Components
Time and Space Scale
Experiments
Electrostatics
Long-Range Interaction
Short-Range Interaction
Boundary Conditions
Particle-Based Simulation
Implicit Solvent: Brownian Dynamics
Explicit Solvent: Molecular Dynamics
Flux-Based Simulation
Nernst-Planck Equation
The Poisson-Nernst-Planck (NP) Method
Hierarchical Simulation Schemes
Future Directions and Concluding Remarks
References
5. Wavelets in Chemistry and Chemoinformatics
Preface
Introduction to Wavelets
Fourier Transform
Continuous Fourier Transform
Short-Time Fourier Transformation
Wavelet Transform
Continuous Wavelet Transform
Discrete Wavelet Transform
Wavelet Packet Transform
Wavelets vs. Fourier Transforms: A Summary
Application of Wavelets in Chemistry
Smoothing and Denoising
Signal Feature Isolation
Signal Compression
Quantum Chemistry
Classification, Regression, and QSAR/QSPR
Summary
References
Author Index
Subject Index

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