Numerical Computer Methods, Part D

<p>Editors-In-Chief</p> <p>Contributors to Volume 383</p> <p>Preface</p> <p>Methods In Enzymology</p> <p>Prediction of Protein Structure</p> <p>Overview and Perspective</p> <p>Classifications of Protein Structure</p> <p>Concepts and Evaluations of Protein Predictions</p> <p>Process of Extracting Information about Protein Structure from Sequence</p> <p>Future Directions</p> <p>Modeling and Studying Proteins with Molecular Dynamics</p> <p>Introduction</p> <p>Sampling of CHARMM Capabilities</p> <p>Program Operation Basics</p> <p>Example Analysis</p> <p>Ab Initio Protein Folding Using LINUS</p> <p>Introduction</p> <p>Anatomy of LINUS Simulation</p> <p>Implementation</p> <p>Simulation Examples</p> <p>Conclusion</p> <p>Appendix I</p> <p>Protein Structure Prediction Using Rosetta</p> <p>Introduction</p> <p>Rosetta Strategy</p> <p>De Novo Structure Prediction with Rosetta</p> <p>Structure Prediction by Fragment Assembly</p> <p>Enhancements of Fragment Insertion Strategy</p> <p>Effectiveness of Conformation Modification Operators for Energy Function Optimization</p> <p>Conclusions</p> <p>Supplemental Materials</p> <p>Appendix I</p> <p>Appendix II</p> <p>Poisson–Boltzmann Methods for Biomolecular Electrostatics</p> <p>Introduction</p> <p>Numerical Solution of Poisson–Boltzmann Equation</p> <p>Applications to Biomedical Sciences</p> <p>Conclusions</p> <p>Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm</p> <p>Introduction</p> <p>Replica Exchange Molecular Dynamics</p> <p>Practical Issues</p> <p>Appendix</p> <p>DNA Microarray Time Series Analysis: Automated Statistical Assessment of Circadian Rhythms in Gene Expression Patterning</p> <p>Introduction</p> <p>Statistical Assessment of Daily Rhythms in Microarray Data</p> <p>Simulation Procedure</p> <p>Comparisons of Analytical Results</p> <p>Summary</p> <p>Molecular Simulations of Diffusion and Association in Multimacromolecular Systems</p> <p>Introduction</p> <p>Theoretical Aspects</p> <p>Practical Aspects</p> <p>Some Example Applications</p> <p>Conclusion</p> <p>Modeling Lipid–Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and Rafts</p> <p>Introduction</p> <p>Theoretical Models</p> <p>Simulation Methods</p> <p>Results</p> <p>Summary and Perspectives</p> <p>Idealization and Simulation of Single Ion Channel Data</p> <p>Introduction</p> <p>Noise</p> <p>Filtering</p> <p>Missed Events</p> <p>Subconductance Levels</p> <p>Models</p> <p>Analysis Methods</p> <p>Simulation</p> <p>Idealization</p> <p>Interpretation</p> <p>Performance</p> <p>Statistical Error in Isothermal Titration Calorimetry</p> <p>Introduction</p> <p>Variance–Covariance Matrix in Least Squares</p> <p>Monte Carlo Computational Methods</p> <p>Van't Hoff Analysis of K°(T): Least-Squares Demonstration</p> <p>Isothermal Titration Calorimetry</p> <p>Calorimetric Versus Van't Hoff ΔH° from ITC</p> <p>Conclusion</p> <p>Analysis of Circular Dichroism Data</p> <p>Introduction</p> <p>Summary of Methods to Obtain Secondary Structure of Proteins from Circular Dichroism Data</p> <p>Determination of Thermodynamics of Protein Folding/Unfolding from CD Data</p> <p>Determination of Binding Constants from CD Data</p> <p>Conclusion</p> <p>Appendix I</p> <p>Computation and Analysis of Protein Circular Dichroism Spectra</p> <p>Introduction</p> <p>Basic Definitions</p> <p>Computation of Protein CD</p> <p>Analysis of Protein CD</p> <p>Model Comparison Methods</p> <p>Introduction</p> <p>Statistical Foundations of Model Comparison</p> <p>Model Comparison Methods</p> <p>Model Comparison at Work</p> <p>Conclusion</p> <p>Practical Robust Fit of Enzyme Inhibition Data</p> <p>Introduction</p> <p>Theory</p> <p>Numerical Example</p> <p>Implementation Notes</p> <p>Conclusions</p> <p>Measuring Period of Human Biological Clock: Infill Asymptotic Analysis of Harmonic Regression Parameter Estimates</p> <p>Introduction</p> <p>Theory</p> <p>Proof</p> <p>Proof</p> <p>Proof</p> <p>Data Analysis</p> <p>Discussion</p> <p>Appendix I: Outline of Proof of Proposition 1</p> <p>Appendix II: Proof of Lemma 1</p> <p>Appendix III: Proof of Lemma 2</p> <p>Bayesian Methods to Improve Sample Size Approximations</p> <p>Introduction</p> <p>Bayesian Inference</p> <p>Deriving Sample Size Formulas</p> <p>Choosing Prior Distributions</p> <p>Gain from Using Prior Information</p> <p>Examples</p> <p>Conclusion</p> <p>Distribution Functions from Moments and the Maximum-Entropy Method</p> <p>Introduction</p> <p>Ligand Binding: Moments</p> <p>Maximum-Entropy Distributions</p> <p>Ligand Binding: Distribution Functions</p> <p>Enthalpy Distributions</p> <p>Self-Association Distributions</p> <p>Author Index</p> <p>Subject Index</p>