Numerical Computer Methods, Part D

Edited by Ludwig Brand and Michael L. Johnson

• Editors-In-ChiefContributors to Volume 383PrefaceMethods In EnzymologyPrediction of Protein StructureOverview and PerspectiveClassifications of Protein StructureConcepts and Evaluations of Protein PredictionsProcess of Extracting Information about Protein Structure from SequenceFuture DirectionsModeling and Studying Proteins with Molecular DynamicsIntroductionSampling of CHARMM CapabilitiesProgram Operation BasicsExample AnalysisAb Initio Protein Folding Using LINUSIntroductionAnatomy of LINUS SimulationImplementationSimulation ExamplesConclusionAppendix IProtein Structure Prediction Using RosettaIntroductionRosetta StrategyDe Novo Structure Prediction with RosettaStructure Prediction by Fragment AssemblyEnhancements of Fragment Insertion StrategyEffectiveness of Conformation Modification Operators for Energy Function OptimizationConclusionsSupplemental MaterialsAppendix IAppendix IIPoisson–Boltzmann Methods for Biomolecular ElectrostaticsIntroductionNumerical Solution of Poisson–Boltzmann EquationApplications to Biomedical SciencesConclusionsAtomic Simulations of Protein Folding, Using the Replica Exchange AlgorithmIntroductionReplica Exchange Molecular DynamicsPractical IssuesAppendixDNA Microarray Time Series Analysis: Automated Statistical Assessment of Circadian Rhythms in Gene Expression PatterningIntroductionStatistical Assessment of Daily Rhythms in Microarray DataSimulation ProcedureComparisons of Analytical ResultsSummaryMolecular Simulations of Diffusion and Association in Multimacromolecular SystemsIntroductionTheoretical AspectsPractical AspectsSome Example ApplicationsConclusionModeling Lipid–Sterol Bilayers: Applications to Structural Evolution, Lateral Diffusion, and RaftsIntroductionTheoretical ModelsSimulation MethodsResultsSummary and PerspectivesIdealization and Simulation of Single Ion Channel DataIntroductionNoiseFilteringMissed EventsSubconductance LevelsModelsAnalysis MethodsSimulationIdealizationInterpretationPerformanceStatistical Error in Isothermal Titration CalorimetryIntroductionVariance–Covariance Matrix in Least SquaresMonte Carlo Computational MethodsVan't Hoff Analysis of K°(T): Least-Squares DemonstrationIsothermal Titration CalorimetryCalorimetric Versus Van't Hoff ΔH° from ITCConclusionAnalysis of Circular Dichroism DataIntroductionSummary of Methods to Obtain Secondary Structure of Proteins from Circular Dichroism DataDetermination of Thermodynamics of Protein Folding/Unfolding from CD DataDetermination of Binding Constants from CD DataConclusionAppendix IComputation and Analysis of Protein Circular Dichroism SpectraIntroductionBasic DefinitionsComputation of Protein CDAnalysis of Protein CDModel Comparison MethodsIntroductionStatistical Foundations of Model ComparisonModel Comparison MethodsModel Comparison at WorkConclusionPractical Robust Fit of Enzyme Inhibition DataIntroductionTheoryNumerical ExampleImplementation NotesConclusionsMeasuring Period of Human Biological Clock: Infill Asymptotic Analysis of Harmonic Regression Parameter EstimatesIntroductionTheoryProofProofProofData AnalysisDiscussionAppendix I: Outline of Proof of Proposition 1Appendix II: Proof of Lemma 1Appendix III: Proof of Lemma 2Bayesian Methods to Improve Sample Size ApproximationsIntroductionBayesian InferenceDeriving Sample Size FormulasChoosing Prior DistributionsGain from Using Prior InformationExamplesConclusionDistribution Functions from Moments and the Maximum-Entropy MethodIntroductionLigand Binding: MomentsMaximum-Entropy DistributionsLigand Binding: Distribution FunctionsEnthalpy DistributionsSelf-Association DistributionsAuthor IndexSubject Index