Reviews in Computational Chemistry, Volume 22

by Lipkowitz, Kenny B.; Cundari, Thomas R.; Gillet, Valerie J.; Boyd, Donald B.

• ISBN13: 9780471779384
• ISBN10: 0471779385
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-02-03
• Publisher: Wiley-VCH

Summary

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.

Author Biography

<b>Kenny B. Lipkowitz</b> is a recently retired Professor of Chemistry from North Dakota&#160;State University. <p> <b>Valerie Gillet</b> is a Professor in the Department of Information Studies at the University of Sheffield. <p> <b>Tom Cundari</b> is Professor of Chemistry at the University of North Texas.

Table of Contents

1. Protein Structure Classification	1	(56)
Patrice Koehl
Introduction	1	(3)
Classification and Biology	2	(1)
The Biomolecular Revolution	2	(2)
Basic Principles of Protein Structure	4	(10)
Visualization	4	(1)
Protein Building Blocks	5	(1)
Protein Structure Hierarchy	5	(2)
Three Types of Proteins	7	(2)
Geometry of Globular Proteins	9	(3)
Protein Domains	12	(1)
Resources on Protein Structures	13	(1)
Protein Structure Comparison	14	(23)
Automatic Identification of Protein Structural Domains	14	(2)
The Rigid-Body Transformation Problem	16	(7)
Protein Structure Superposition	23	(8)
cRMS: An Ambiguous Measure of Similarity	31	(2)
Differential Geometry and Protein Structure Comparison	33	(3)
Upcoming Challenges for Protein Structure Comparison	36	(1)
Protein Structure Classification	37	(8)
The Structure Classification of Proteins (SCOP)	40	(2)
The CATH Classification	42	(1)
The DALI Domain Dictionary (DDD)	43	(1)
Comparing SCOP, CATH, and DDD	43	(2)
Conclusions	45	(1)
Acknowledgments	46	(1)
Appendix	47	(1)
References	48	(9)
2. Comparative Protein Modeling	57	(112)
Emilio Xavier Esposito, Dror Tobi, and Jeffry D. Madura
Introduction	57	(3)
Anatomy of a Comparative Model	60	(1)
Step 1: Searching for Related Sequences and Structures	61	(23)
Expert Protein Analysis System (ExPASy)	62	(3)
BLAST and PSI-BLAST	65	(3)
Protein Data Bank (PDB)	68	(2)
Sequence Alignment and Modeling System with Hidden Markov Models	70	(3)
Threading	73	(5)
Threader	78	(2)
Example: Finding Related Sequences and 3-D Structures	80	(4)
Step 2: Sequence Alignment	84	(20)
Preparing the Sequences	87	(3)
Alignment Basics	90	(1)
Similarity Matrices	91	(4)
Clustal	95	(4)
Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee)	99	(1)
Divide-and-Conquer Alignment (DCA)	100	(1)
Example: Aligning Sequences	101	(3)
Step 3: Selecting Templates and Improving Alignments	104	(7)
Selecting Templates	104	(3)
Improving Sequence Alignments With Primary and Secondary Structure Analysis	107	(4)
Example: Aligning the Target to the Selected Template	111	(1)
Step 4: Constructing Protein Models	111	(13)
Satisfaction of Spatial Restraints	113	(2)
Segment Match Modeling	115	(3)
Multiple Template Method	118	(1)
3D-JIGSAW	119	(2)
Overall Protein Model Construction Methods	121	(1)
Example: Constructing a Protein Model	122	(2)
Step 5: Refinement of Protein Models	124	(14)
Side-Chains with Rotamer Library (SCWRL)	125	(7)
Energy Minimization	132	(1)
Molecular Dynamics	133	(2)
Molecular Dynamics with Simulated Annealing	135	(3)
Step 6: Evaluating Protein Models	138	(16)
PRO CHECK	138	(2)
Verify3D	140	(1)
ERRAT	141	(1)
Protein Structure Analysis (ProSa)	142	(2)
Protein Volume Evaluation (PROVE)	144	(2)
Model Clustering Analysis	146	(2)
Example: Evaluation of Protein Models	148	(6)
Conclusions	154	(1)
References	155	(14)
3. Simulations of Protein Folding	169	(60)
Joan-Emma Shea, Miriam R. Friedel, and Andrij Baumketner
Introduction	169	(3)
Theoretical Framework	172	(7)
Energy Landscape Theory	172	(3)
Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders	175	(4)
Protein Models	179	(22)
Introduction and General Simulation Techniques	179	(2)
Coarse-Grained Protein Models	181	(9)
Fully Atomic Simulations	190	(11)
Advanced Topics: The Transition State Ensemble for Folding	201	(18)
Transition State and Two-State Kinetics	202	(2)
Methods for Identifying the TSE	204	(15)
Conclusions and Future Directions	219	(1)
Acknowledgments	219	(1)
References	220	(9)
4. The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods	229	(66)
Marco Saraniti, Shela Aboud, and Robert Eisenberg
Introduction	229	(14)
System Components	231	(10)
Time and Space Scale	241	(1)
Experiments	242	(1)
Electrostatics	243	(20)
Long-Range Interaction	245	(13)
Short-Range Interaction	258	(3)
Boundary Conditions	261	(2)
Particle-Based Simulation	263	(10)
Implicit Solvent: Brownian Dynamics	264	(3)
Explicit Solvent: Molecular Dynamics	267	(6)
Flux-Based Simulation	273	(9)
Nernst–Planck Equation	274	(4)
The Poisson–Nernst–Planck (NP) Method	278	(4)
Hierarchical Simulation Schemes	282	(1)
Future Directions and Concluding Remarks	283	(1)
References	284	(11)
5. Wavelets in Chemistry and Chemoinformatics	295	(36)
C. Matthew Sundling, Nagamani Sukumar, Hongmei Zhang, Mark J. Embrechts, and Curt M. Breneman
Preface	295	(1)
Introduction to Wavelets	296	(13)
Fourier Transform	297	(1)
Continuous Fourier Transform	297	(1)
Short-Time Fourier Transformation	298	(2)
Wavelet Transform	300	(1)
Continuous Wavelet Transform	301	(2)
Discrete Wavelet Transform	303	(4)
Wavelet Packet Transform	307	(1)
Wavelets vs. Fourier Transforms: A Summary	308	(1)
Application of Wavelets in Chemistry	309	(12)
Smoothing and Denoising	309	(3)
Signal Feature Isolation	312	(1)
Signal Compression	313	(1)
Quantum Chemistry	314	(2)
Classification, Regression, and QSAR/QSPR	316	(5)
Summary	321	(1)
References	321	(10)
Author Index	331	(18)
Subject Index	349