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Computational systems pharmacology and toxicology

Systems Biology Approaches in Pharmacology and ToxicologyIntroductionSystems ToxicologyChemical ToxicidesSingle-Target Toxicity ConceptsToxicological Profiling for Potential Adverse ReactionsToxicological Concepts for Safer Chemical DesignBiomarkersEnvironmental ToxicologyAdverse Outcome PathwayExpanding Exposure ConceptsExposomeSystems and Network PharmacologySecondary Pharmacology and Off-Target EffectsPrediction of Potential Adverse EffectsConclusionsReferencesDatabases Facilitating Systems Biology Approaches in ToxicologyIntroductionCategorized Lists of Databases for Systems ToxicologyTOXNET Databases (Including Those with Direct Links from TOXNET)US EPA Chemical Toxicity DatabasesNational Toxicology Program DatabasesAdditional Toxicity DatabasesChemical-Gene-Protein DatabasesPathway-Network DatabasesChemistry, Structural Alert, and QSAR Databases and ToolsDrug and Drug Target DatabasesWebsites with Extensive Links to Databases and ToolsConclusionsReferencesTools for Green Molecular Design to Reduce Toxicological RiskIntroductionPhysiochemical, Genotoxicity, and Blood-Brain Barrier Passage Properties of ChemicalsTooIs for Green Molecular DesignExpert SystemsDecision TreesQSARTooIsRepresentative ToolsACD Percepta ( Predictor ( DesignerDerek and Meteor Nexus from Lhasa Limited ( ( QSAR ToolboxToxtree ( Suite (Marvin Sketch and Metabolizer) ( ( (Analog Identification Methodology) ( identification-methodology-aim-tool)Chemspider ( ( StudyThe Design of Ideal Tools for ChemistsConclusionsReferencesLinking Environmental Exposure to Toxicity*IntroductionThe AOP Framework: An Organizing Principle for Toxicological DataAOP Knowledge ManagementPhases of AOP DevelopmentData Resources for AOP DevelopmentEnvironmental Exposure and Pharmacokinetic Considerations for Adverse Outcome DevelopmentThe AEP Framework: An Organizing Principle for Exposure DataData resources for AEP developmentAEP-AOP Integration for Linking Toxicity to Exposure: Applications of the AOP and AEP Frameworks for Risk Assessments and Chemical Management Decision MakingConclusions and Future DirectionsReferencesLinking Drug or Phytochemical Exposure to ToxicityIntroductionPharmacokinetic and Toxicokinetic ModelsStructural ModelsCompartmental ModelsPhysiological ModelsVariance ModelsOther Modeling MethodologiesPK/PD RelationshipsMathematical Description of Pharmacodynamic EffectsDirect Effects and Effect CompartmentsIndirect EffectsCombined PK/PD and TK/TD ModelingModeling Pharmacodynamics in the Absence of Pharmacokinetic Data: K-PD ModelsModeling Drug Interactions with PhytochemicalsInhibition of MetabolismInduction of MetabolismEnhancement of AbsorptionInhibition of AbsorptionModeling of Pharmacodynamic InteractionsConclusionsReferencesChemical Similarity, Shape Matching and QSARIntroductionMolecular Similarity, Chemical Spaces and Activity LandscapesMolecular Similarity: Concept and DefinitionsMolecular Similarity ConceptApplicability of Molecular Similarity MeasuresStructure Representations for Molecular Similarity AnalysisMolecular Similarity FunctionsChemical Spaces and Activity LandscapesApplications of Molecular Similarity AnalysisSimilarity-Based Virtual ScreeningActivity PredictionClustering, Networks and DiversityQuantitative Structure-Activity/Property Relationships (QSAR/QSPR)Congeneric Series and Consistent MechanismsDiverse Series and Big DataPrediction of ADMETPropertiesPrediction of Potential Drug TargetsPrediction of Activity Towards Individual TargetsPrediction of Physico-Chemical PropertiesOpen Web-Based QSAR/QSPR ServicesConclusionAcknowledgementsReferencesIn silico Chemical-Protein Docking and Molecular DynamicsIntroductionMolecular Docking: Overview and ApplicationsGenetic AlgorithmsMonte Carlo ProcedureMatching AlgorithmsScoring Ligand PosesInverse DockingCase Study: Using In silico Docking to Investigate Interactions of 1,3-Dinitrobenzene with Adenosine DeaminaseCase Study: Using In silico Docking to Assess Binding of Bisphenol-A to Estrogen-Related Receptor-yMolecular DynamicsRunning MD SimulationsAnalysis of MD TrajectoriesCase Study: Gaining Insights into the Conformational Dynamics of Human Neuropathy Target Esterase via MD Simulations of its Catalytic Domain Homologue Patatin-17 in Complex with Organophosphorous CompoundsReferencesComputational Tools for Chemical Toxicity Testing and Risk Assessment Under the Framework of Adverse Outcome PathwaysIntroductionThe AOP ConceptQuantitative Methods in Traditional Apical Endpoints TestingPBPK Modeling and In vitro to In vivo ExtrapolationSAR ModelingComputational Modeling of Toxicity PathwaysConcept of Toxicity PathwaysPurpose of Modeling Toxicity PathwaysHow to Model Toxicity PathwaysCase StudiesEducation on Computational ToxicologyPathway Modeling Software ToolsReferencesIn silico Toxicology: An Overview of Toxicity Databases, Prediction Methodologies, and Expert ReviewIntroductionToxicity DatabasesOverviewDatabase OrganizationGenetic Toxicity and CarcinogenicityReproductive and Developmental ToxicityAcute and Repeated Dose ToxicityIn silico MethodologiesOverviewExpert AlertsQSARsRead-AcrossExpert ReviewsAssessing Experimental DataDrawing Conclusions from Multiple SystemsReviews Accepting or Refuting An In silico ResultDocumenting In silico ResultsConclusionsReferencesData Sources for Herbal and Traditional MedicinesIntroductionTCM DatabasesChem-TCM (Chemical Database of Traditional Chinese Medicine)HIT (Linking Herbal Active Ingredients to Targets)TCMSP (Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform)TCMGeneDIT (A Database for Associated TCM, Gene and Disease Information Using Text Mining}TCMID (Traditional Chinese Medicine Integrative Database for Herb Molecular Mechanism Analysis)TTD (Therapeutic Target Database)Omics Data in TCMGenomics in TCMTranscriptomics in TCMProteomics in TCMMetabonomics in TCMSummaryReferencesNetwork Pharmacology Research Approaches for Chinese Herbal MedicinesIntroductionModernization of TCMConcept of Network PharmacologyNetwork Pharmacology in TCM ResearchNetwork Pharmacology in the Understanding of Herb-Drug InteractionsPharmacogenomics in TCMTCMs in Clinical TrialsThe Future of Network Pharmacology in Traditional MedicineConclusionReferencesChemical-Disease Category Linkage (CDCL): Computational Methods Linking Traditional Chinese Medicines and Western TherapeuticsIntroductionDatabases for CDCL Information and StudyTCM and Chemical ConstituentsTCM Classification and Systems ApproachWestern TherapeuticsTherapeutic Targets and Protein InteractionsPathway AnalysisTCM ClassificationsActive Ingredients in HerbsWind ColdHeat (Blood)Tonify QiTonify BloodOpen Access Tools for CDCL InformaticsComputational CDCL Studies with Commercial ToolsHerb-Drug InteractionsPharmacokinetic InteractionsPharmacogenomic-Related InteractionsCombination Therapies and Future DirectionsConclusionsReferencesEducational Programs for Computational Toxicology and PharmacologyIntroductionHistorical Context: Computational ToxicologyBackgroundPrograms at University of California Berkeley and University of MichiganInquiry-Based Science CoursesCurrent Computational Toxicology CoursesToxicology TutorialsCourse ConceptsCase StudiesChemical Structural Features Determine Biological EffectsHerbal Traditional MedicinesCourse ProjectsStarting ProjectsTypical Project CategoriesTherapeutics vs. Environmental ChemicalsChallenges in Computational ToxicologyHazard-Based Information GatheringSample Project: The Chemical of Concern QuestionHealth Effects InquiryEndpoints for Breast CancerProject QuestionCourse Projects Presented and PublishedProjects Presented at National Scientific MeetingsSociety of Environmental Toxicology and Chemistry (SETAC)National Society of Toxicology Through 2015Projects from the Courses Published in JournalsComputational Pharmacology as Part of the Principles of Drug ActionConclusionReferences
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