<b>1. Protein Structure Classification</b> (Patrice Koehl). <p>Introduction.</p> <p>Classification and Biology.</p> <p>The Biomolecular Revolution.</p> <p>Basic Principles of Protein Structure.</p> <p>Visualization.</p> <p>Protein Building Blocks.</p> <p>Protein Structure Hierarchy.</p> <p>Three Types of Proteins.</p> <p>Geometry of Globular Proteins.</p> <p>Protein Domains.</p> <p>Resources on Protein Structures.</p> <p>Protein Structure Comparison.</p> <p>Automatic Identification of Protein Structural Domains.</p> <p>The Rigid-Body Transformation Problem.</p> <p>Protein Structure Superposition.</p> <p>cRMS: An Ambiguous Measure of Similarity.</p> <p>Differential Geometry and Protein Structure Comparison.</p> <p>Upcoming Challenges for Protein Structure Comparison.</p> <p>Protein Structure Classification.</p> <p>The Structure Classification of Proteins (SCOP).</p> <p>The CATH Classification.</p> <p>The DALI Domain Dictionary (DDD).</p> <p>Comparing SCOP, CATH, and DDD.</p> <p>Conclusions.</p> <p>Acknowledgments.</p> <p>Appendix.</p> <p>References.</p> <p><b>2. Comparative Protein Modeling</b> (Emilio Xavier Esposito, Dror Tobi, and Jeffry D. Madura).</p> <p>Introduction.</p> <p>Anatomy of a Comparative Model.</p> <p>Step 1: Searching for Related Sequences and Structures.</p> <p>Expert Protein Analysis System (ExPASy).</p> <p>BLAST and PSI-BLAST.</p> <p>Protein Data Bank (PDB).</p> <p>Sequence Alignment and Modeling System with Hidden Markov Models.</p> <p>Threading.</p> <p>Threader.</p> <p>Example: Finding Related Sequences and 3-D Structures.</p> <p>Step 2: Sequence Alignment.</p> <p>Preparing the Sequences.</p> <p>Alignment Basics.</p> <p>Similarity Matrices.</p> <p>Clustal.</p> <p>Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee).</p> <p>Divide-and-Conquer Alignment (DCA).</p> <p>Example: Aligning Sequences.</p> <p>Step 3: Selecting Templates and Improving Alignments.</p> <p>Selecting Templates.</p> <p>Improving Sequence Alignments With Primary and Secondary Structure Analysis.</p> <p>Example: Aligning the Target to the Selected Template.</p> <p>Step 4: Constructing Protein Models.</p> <p>Satisfaction of Spatial Restraints.</p> <p>Segment Match Modeling.</p> <p>Multiple Template Method.</p> <p>3D-JIGSAW.</p> <p>Overall Protein Model Construction Methods.</p> <p>Example: Constructing a Protein Model.</p> <p>Step 5: Refinement of Protein Models.</p> <p>Side-Chains with Rotamer Library (SCWRL).</p> <p>Energy Minimization.</p> <p>Molecular Dynamics.</p> <p>Molecular Dynamics with Simulated Annealing.</p> <p>Step 6: Evaluating Protein Models.</p> <p>PROCHECK.</p> <p>Verify3D.</p> <p>ERRAT.</p> <p>Protein Structure Analysis (ProSa).</p> <p>Protein Volume Evaluation (PROVE).</p> <p>Model Clustering Analysis.</p> <p>Example: Evaluation of Protein Models.</p> <p>Conclusions.</p> <p>References.</p> <p><b>3. Simulations of Protein Folding</b> (Joan-Emma Shea, Miriam R. Friedel, and Andrij Baumketner).</p> <p>Introduction.</p> <p>Theoretical Framework.</p> <p>Energy Landscape Theory.</p> <p>Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders.</p> <p>Protein Models.</p> <p>Introduction and General Simulation Techniques.</p> <p>Coarse-Grained Protein Models.</p> <p>Fully Atomic Simulations.</p> <p>Advanced Topics: The Transition State Ensemble for Folding.</p> <p>Transition State and Two-State Kinetics.</p> <p>Methods for Identifying the TSE.</p> <p>Conclusions and Future Directions.</p> <p>Acknowledgments.</p> <p>References.</p> <p><b>4. The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods</b> (Marco Saraniti, Shela Aboud, and Robert Eisenberg).</p> <p>Introduction.</p> <p>System Components.</p> <p>Time and Space Scale.</p> <p>Experiments.</p> <p>Electrostatics.</p> <p>Long-Range Interaction.</p> <p>Short-Range Interaction.</p> <p>Boundary Conditions.</p> <p>Particle-Based Simulation.</p> <p>Implicit Solvent: Brownian Dynamics.</p> <p>Explicit Solvent: Molecular Dynamics.</p> <p>Flux-Based Simulation.</p> <p>Nernst–Planck Equation.</p> <p>The Poisson–Nernst–Planck (NP) Method.</p> <p>Hierarchical Simulation Schemes.</p> <p>Future Directions and Concluding Remarks.</p> <p>References.</p> <p><b>5. Wavelets in Chemistry and Chemoinformatics</b> (C. Matthew Sundling, Nagamani Sukumar, Hongmei Zhang, Mark J. Embrechts, and Curt M. Breneman).</p> <p>Preface.</p> <p>Introduction to Wavelets.</p> <p>Fourier Transform.</p> <p>Continuous Fourier Transform.</p> <p>Short-Time Fourier Transformation.</p> <p>Wavelet Transform.</p> <p>Continuous Wavelet Transform.</p> <p>Discrete Wavelet Transform.</p> <p>Wavelet Packet Transform.</p> <p>Wavelets vs. Fourier Transforms: A Summary.</p> <p>Application of Wavelets in Chemistry.</p> <p>Smoothing and Denoising.</p> <p>Signal Feature Isolation.</p> <p>Signal Compression.</p> <p>Quantum Chemistry.</p> <p>Classification, Regression, and QSAR/QSPR.</p> <p>Summary.</p> <p>References.</p> <p><b>Author Index.</b></p> <p><b>Subject Index.</b></p>