Reviews in Computational Chemistry, Volume 22

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.

Kenny B. Lipkowitz is a recently retired Professor of Chemistry from North Dakota State University. Valerie Gillet is a Professor in the Department of Information Studies at the University of Sheffield. Tom Cundari is Professor of Chemistry at the University of North Texas.

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

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Reviews in Computational Chemistry, Volume 22

Summary

Author Biography

Table of Contents

Supplemental Materials