Reviews in Computational Chemistry, Volumes 1 - 17 Set

, by Lipkowitz, Kenny B.; Boyd, Donald B.

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ISBN: 9780471219224 | 0471219223
Cover: Hardcover
Copyright: 1/29/2002

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This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Volume 23 covers linear scaling methods for quantum chemistry variational transition state theory, coarse grain modeling of polymers, support vector machines, conical intersections, analysis of information content using shannon entropy and historical insights into how computing evolved in the pharmaceutical industry. Book jacket.

Protein Structure Classification	p. 1
Introduction	p. 1
Classification and Biology	p. 2
The Biomolecular Revolution	p. 2
Basic Principles of Protein Structure	p. 4
Visualization	p. 4
Protein Building Blocks	p. 5
Protein Structure Hierarchy	p. 5
Three Types of Proteins	p. 7
Geometry of Globular Proteins	p. 9
Protein Domains	p. 12
Resources on Protein Structures	p. 13
Protein Structure Comparison	p. 14
Automatic Identification of Protein Structural Domains	p. 14
The Rigid-Body Transformation Problem	p. 16
Protein Structure Superposition	p. 23
cRMS: An Ambiguous Measure of Similarity	p. 31
Differential Geometry and Protein Structure Comparison	p. 33
Upcoming Challenges for Protein Structure Comparison	p. 36
Protein Structure Classification	p. 37
The Structure Classification of Proteins (SCOP)	p. 40
The CATH Classification	p. 42
The DALI Domain Dictionary (DDD)	p. 43
Comparing SCOP, CATH, and DDD	p. 43
Conclusions	p. 45
Acknowledgments	p. 46
Appendix	p. 47
References	p. 48
Comparative Protein Modeling	p. 57
Introduction	p. 57
Anatomy of a Comparative Model	p. 60
Searching for Related Sequences and Structures	p. 61
Expert Protein Analysis System (ExPASy)	p. 62
Blast and PSI-Blast	p. 65
Protein Data Bank (PDB)	p. 68
Sequence Alignment and Modeling System with Hidden Markov Models	p. 70
Threading	p. 73
Threader	p. 78
Example: Finding Related Sequences and 3-D Structures	p. 80
Sequence Alignment	p. 84
Preparing the Sequences	p. 87
Alignment Basics	p. 90
Similarity Matrices	p. 91
Clustal	p. 95
Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee)	p. 99
Divide-and-Conquer Alignment (DCA)	p. 100
Example: Aligning Sequences	p. 101
Selecting Templates and Improving Alignments	p. 104
Selecting Templates	p. 104
Improving Sequence Alignments With Primary and Secondary Structure Analysis	p. 107
Example: Aligning the Target to the Selected Template	p. 111
Constructing Protein Models	p. 111
Satisfaction of Spatial Restraints	p. 113
Segment Match Modeling	p. 115
Multiple Template Method	p. 118
3D-Jigsaw	p. 119
Overall Protein Model Construction Methods	p. 121
Example: Constructing a Protein Model	p. 122
Refinement of Protein Models	p. 124
Side-Chains with Rotamer Library (SCWRL)	p. 125
Energy Minimization	p. 132
Molecular Dynamics	p. 133
Molecular Dynamics with Simulated Annealing	p. 135
Evaluating Protein Models	p. 138
Procheck	p. 138
Verify3D	p. 140
Errat	p. 141
Protein Structure Analysis (ProSa)	p. 142
Protein Volume Evaluation (PROVE)	p. 144
Model Clustering Analysis	p. 146
Example: Evaluation of Protein Models	p. 148
Conclusions	p. 154
References	p. 155
Simulations of Protein Folding	p. 169
Introduction	p. 169
Theoretical Framework	p. 172
Energy Landscape Theory	p. 172
Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders	p. 175
Protein Models	p. 179
Introduction and General Simulation Techniques	p. 179
Coarse-Grained Protein Models	p. 181
Fully Atomic Simulations	p. 190
Advanced Topics: The Transition State Ensemble for Folding	p. 201
Transition State and Two-State Kinetics	p. 202
Methods for Identifying the TSE	p. 204
Conclusions and Future Directions	p. 219
Acknowledgments	p. 219
References	p. 220
The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods	p. 229
Introduction	p. 229
System Components	p. 231
Time and Space Scale	p. 241
Experiments	p. 242
Electrostatics	p. 243
Long-Range Interaction	p. 245
Short-Range Interaction	p. 258
Boundary Conditions	p. 261
Particle-Based Simulation	p. 263
Implicit Solvent: Brownian Dynamics	p. 264
Explicit Solvent: Molecular Dynamics	p. 267
Flux-Based Simulation	p. 273
Nernst-Planck Equation	p. 274
The Poisson-Nernst-Planck (NP) Method	p. 278
Hierarchical Simulation Schemes	p. 282
Future Directions and Concluding Remarks	p. 283
References	p. 284
Wavelets in Chemistry and Chemoinformatics	p. 295
Preface	p. 295
Introduction to Wavelets	p. 296
Fourier Transform	p. 297
Continuous Fourier Transform	p. 297
Short-Time Fourier Transformation	p. 298
Wavelet Transform	p. 300
Continuous Wavelet Transform	p. 301
Discrete Wavelet Transform	p. 303
Wavelet Packet Transform	p. 307
Wavelets vs. Fourier Transforms: A Summary	p. 308
Application of Wavelets in Chemistry	p. 309
Smoothing and Denoising	p. 309
Signal Feature Isolation	p. 312
Signal Compression	p. 313
Quantum Chemistry	p. 314
Classification, Regression, and QSAR/QSPR	p. 316
Summary	p. 321
References	p. 321
Author Index	p. 331
Subject Index	p. 349
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Reviews in Computational Chemistry, Volumes 1 - 17 Set

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