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Reviews in Computational Chemistry / Edition 1
     

Reviews in Computational Chemistry / Edition 1

by Kenny B. Lipkowitz, Donald B. Boyd
 

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ISBN-10: 0471186392

ISBN-13: 9780471186397

Pub. Date: 11/14/1996

Publisher: Wiley

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

Overview

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.

Product Details

ISBN-13:
9780471186397
Publisher:
Wiley
Publication date:
11/14/1996
Series:
Reviews in Computational Chemistry Series , #9
Pages:
316
Product dimensions:
6.30(w) x 9.51(h) x 0.87(d)

Table of Contents


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

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