Course Content
Before You Start: Book Club Orientation
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Promo
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Book Club System: How It Works & How You Win
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computational-toxicology-2013
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computational-toxicology-2013
Chapter 1 Methods for Building QSARs
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Abstract
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1 Introduction
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2 Biological Data
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3 Molecular Descriptors
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3 2 2D Molecular Descriptors
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Agent Based
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4 Model Computation
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5 Model Diagnostics
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6 Model Performance Estimation
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7 Interpreting the Models
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8 Concluding Remarks
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Chapter 2 Accessing and Using Chemical Databases
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Abstract
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1 Introduction
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2 Materials
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3 Methods
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4 Examples
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4 2 OASIS Centralized Database
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4 3 The Danish QSAR Database Online
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5 Relational Databases
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6 Examples of Chemical Database Resources Online
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Chapter 3 From QSAR to QSIIR Searching for Enhanced Computational Toxicology Models
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Abstract
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1 Introduction
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2 Availability of Large Compound Collections for In Vivo and In Vitro Toxicity Evaluation
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3 QSAR and Current Challenge of Computational Toxicology
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4 Quantitative Structure In Vitro–In Vivo Relationship
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5 Case Studies 5 1 Using “Hybrid” Descriptors for QSIIR Modeling of Rodent Carcinogenicity
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5.2
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6 Conclusion
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Chapter 4 Mutagenicity, Carcinogenicity, and Other End points
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Abstract
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1 Introduction
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2 Structure–Activity Relationships and the Prediction of Toxicological End points
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3 Sar Based Expert Systems
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3 2 Toxtree
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3 3 OECD QSAR Application Toolbox
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4 Support Tools for Structure–Activity Relationships Work
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4 2 Databases on Chemical Toxicological
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Chapter 5 Classification Models for Safe Drug Molecules
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Abstract
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1 Introduction
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2 Materials and Methods
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2 2 Pattern Recognition Pattern recognition is a term
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2 3 Cluster Analysis
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2 4 Principal
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2 7 Ensemble method utilizes a combination of techniques for con
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2 8 Bayes Classifier 2 9 Moving Average Analysis
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3 Conclusion
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Chapter 6 QSAR and Metabolic Assessment Tools
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QSAR and Metabolic Assessment Tools
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1 Introduction
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2 Materials 2 1 CAESAR 2 2 Derek for
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2 3 HazardExpert 2 4 Lazar 2 5 Meteor
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2 6 OECD QSAR Toolbox The OECD QSAR Toolbox is a stand alone software application
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2 9 ToxBoxes 2 10 Toxtree
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3 Methods 3 1 Stepwise
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4 Case Studies on the Application of Computational Methods
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4 2 5 General Conclusions for 2 Aminoacetophenone
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5 Concluding Remarks
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Chapter 7 Gene Expression Networks
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Abstract
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2 Materials and Methods
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2 2 Accessing Publicly Available Gene
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2 3 Identifying Toxicologically Relevant Gene Expression Networks 2 3 1 Gene Set or
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2 4 Reverse Engineering Gene Expression Networks
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3 Examples 3 1 Immune Response Pathways in the Blood Perturbed at Low
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Disclaimer
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Chapter 8 Construction of Cell Type Specific Logic Models of Signaling Networks Using CellNOpt
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Abstract
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1 Introduction
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2 Materials
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3 Methods 3 1 Logic Modeling in CellNOpt
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3 2 Experimental Design of Datasets
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3 3 Loading the Prior Knowledge Network and Data into CellNOpt
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3 4 Training a Logic Model with CellNOpt
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3 5 Model Analysis
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4 Examples 4 1 Simple Toy Example
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4 2 Application to Data From the Hepatocyte Cell Line HepG2
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5 Notes
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Chapter 9 Regulatory Networks
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Abstract
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1 Introduction
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2 Example Detoxification
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3 Method Thomas’
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3 2 Structure Regulatory Graphs
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3 3 Dynamics State Graphs
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4 An Example of Possible
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5 Materials Model Checking
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5 2 CTL to Encode Biological Properties
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5 3 Computer Aided Elaboration of Formal Model
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Chapter 10 Computational Reconstruction of Metabolic Networks from KEGG
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Abstract
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1 Introduction
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2 Materials
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3 Methods
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3 3 Local Database Design
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4 Applications of the Reconstructed
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5 Notes
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Chapter 11 Biomarkers
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Abstract
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1 Introduction
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1 1 Biomarkers of Adverse Drug Reaction
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1 2 Pharmacogenomic Biomarkers for Potential
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1 3 Computational Approaches for Safety Biomarker
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2 Materials 2 1 Animal Study
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3 Methods
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3 1 Best Practices
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3 2 Inferring Human Endpoints from Animal Data
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4 Examples
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4 1 More Complex Problem
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Computational-Toxicology-2013 | Book-Club |
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