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Reviews in Computational Chemistry : v. 1 - Kenny B. Lipkowitz

Reviews in Computational Chemistry

v. 1

By: Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor)

Hardcover Published: 16th May 1990
ISBN: 9780471187288
Number Of Pages: 440

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This book is an account of current developments in computational chemistry, a new multidisciplinary area of research. Experts in computational chemistry, the editors use and develop techniques for computer-assisted molecular design. The core of the text itself deals with techniques for computer-assisted molecular design. The book is suitable for both beginners and experts.<br> <br> In addition, protocols and software for molecular recognition and the relationship between structure and biological activity of drug molecules are discussed in detail. Each chapter includes a mini-tutorial, as well as discussion of advanced topics.<br> <br> Special Feature: The appendix to this book contains an extensive list of available software for molecular modeling.

Protein Structure Classificationp. 1
Introductionp. 1
Classification and Biologyp. 2
The Biomolecular Revolutionp. 2
Basic Principles of Protein Structurep. 4
Visualizationp. 4
Protein Building Blocksp. 5
Protein Structure Hierarchyp. 5
Three Types of Proteinsp. 7
Geometry of Globular Proteinsp. 9
Protein Domainsp. 12
Resources on Protein Structuresp. 13
Protein Structure Comparisonp. 14
Automatic Identification of Protein Structural Domainsp. 14
The Rigid-Body Transformation Problemp. 16
Protein Structure Superpositionp. 23
cRMS: An Ambiguous Measure of Similarityp. 31
Differential Geometry and Protein Structure Comparisonp. 33
Upcoming Challenges for Protein Structure Comparisonp. 36
Protein Structure Classificationp. 37
The Structure Classification of Proteins (SCOP)p. 40
The CATH Classificationp. 42
The DALI Domain Dictionary (DDD)p. 43
Comparing SCOP, CATH, and DDDp. 43
Conclusionsp. 45
Acknowledgmentsp. 46
Appendixp. 47
Referencesp. 48
Comparative Protein Modelingp. 57
Introductionp. 57
Anatomy of a Comparative Modelp. 60
Searching for Related Sequences and Structuresp. 61
Expert Protein Analysis System (ExPASy)p. 62
Blast and PSI-Blastp. 65
Protein Data Bank (PDB)p. 68
Sequence Alignment and Modeling System with Hidden Markov Modelsp. 70
Threadingp. 73
Threaderp. 78
Example: Finding Related Sequences and 3-D Structuresp. 80
Sequence Alignmentp. 84
Preparing the Sequencesp. 87
Alignment Basicsp. 90
Similarity Matricesp. 91
Clustalp. 95
Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee)p. 99
Divide-and-Conquer Alignment (DCA)p. 100
Example: Aligning Sequencesp. 101
Selecting Templates and Improving Alignmentsp. 104
Selecting Templatesp. 104
Improving Sequence Alignments With Primary and Secondary Structure Analysisp. 107
Example: Aligning the Target to the Selected Templatep. 111
Constructing Protein Modelsp. 111
Satisfaction of Spatial Restraintsp. 113
Segment Match Modelingp. 115
Multiple Template Methodp. 118
3D-Jigsawp. 119
Overall Protein Model Construction Methodsp. 121
Example: Constructing a Protein Modelp. 122
Refinement of Protein Modelsp. 124
Side-Chains with Rotamer Library (SCWRL)p. 125
Energy Minimizationp. 132
Molecular Dynamicsp. 133
Molecular Dynamics with Simulated Annealingp. 135
Evaluating Protein Modelsp. 138
Procheckp. 138
Verify3Dp. 140
Erratp. 141
Protein Structure Analysis (ProSa)p. 142
Protein Volume Evaluation (PROVE)p. 144
Model Clustering Analysisp. 146
Example: Evaluation of Protein Modelsp. 148
Conclusionsp. 154
Referencesp. 155
Simulations of Protein Foldingp. 169
Introductionp. 169
Theoretical Frameworkp. 172
Energy Landscape Theoryp. 172
Thermodynamics and Kinetics of Folding: Two-State and Multistate Foldersp. 175
Protein Modelsp. 179
Introduction and General Simulation Techniquesp. 179
Coarse-Grained Protein Modelsp. 181
Fully Atomic Simulationsp. 190
Advanced Topics: The Transition State Ensemble for Foldingp. 201
Transition State and Two-State Kineticsp. 202
Methods for Identifying the TSEp. 204
Conclusions and Future Directionsp. 219
Acknowledgmentsp. 219
Referencesp. 220
The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methodsp. 229
Introductionp. 229
System Componentsp. 231
Time and Space Scalep. 241
Experimentsp. 242
Electrostaticsp. 243
Long-Range Interactionp. 245
Short-Range Interactionp. 258
Boundary Conditionsp. 261
Particle-Based Simulationp. 263
Implicit Solvent: Brownian Dynamicsp. 264
Explicit Solvent: Molecular Dynamicsp. 267
Flux-Based Simulationp. 273
Nernst-Planck Equationp. 274
The Poisson-Nernst-Planck (NP) Methodp. 278
Hierarchical Simulation Schemesp. 282
Future Directions and Concluding Remarksp. 283
Referencesp. 284
Wavelets in Chemistry and Chemoinformaticsp. 295
Prefacep. 295
Introduction to Waveletsp. 296
Fourier Transformp. 297
Continuous Fourier Transformp. 297
Short-Time Fourier Transformationp. 298
Wavelet Transformp. 300
Continuous Wavelet Transformp. 301
Discrete Wavelet Transformp. 303
Wavelet Packet Transformp. 307
Wavelets vs. Fourier Transforms: A Summaryp. 308
Application of Wavelets in Chemistryp. 309
Smoothing and Denoisingp. 309
Signal Feature Isolationp. 312
Signal Compressionp. 313
Quantum Chemistryp. 314
Classification, Regression, and QSAR/QSPRp. 316
Summaryp. 321
Referencesp. 321
Author Indexp. 331
Subject Indexp. 349
Table of Contents provided by Ingram. All Rights Reserved.

ISBN: 9780471187288
ISBN-10: 0471187283
Series: Reviews in Computational Chemistry
Audience: Professional
Format: Hardcover
Language: English
Number Of Pages: 440
Published: 16th May 1990
Country of Publication: US
Dimensions (cm): 24.1 x 16.1  x 2.74
Weight (kg): 0.7
Edition Number: 1

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