Computational Toxicology, 1st ed. 2018
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1800

Language: English

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Computational Toxicology
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Computational Toxicology
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This volume explores techniques that are currently used to understand solid target-specific models in computational toxicology. The chapters are divided into four sections and discuss topics such as molecular descriptors, QSAR and read-across; molecular and data modeling techniques to comply with both scientific and regulatory sides; computational toxicology in drug discovery; and strategies on how to predict various human-health toxicology endpoints. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the methods and software tools used, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and cutting-edge, Computational Toxicology: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this expanding field.

Dedication…

Preface…

Table of Contents…

Contributing Authors…

 

Part I Where We Are and Where We Are Going To


1. Molecular Descriptors For Structure-Activity Applications: A Hands-On Approach

Francesca Grisoni, Davide Ballabio, Roberto Todeschini, and Viviana Consonni 


2. The OECD QSAR Toolbox Starts Its Second Decade

Terry W. Schultz, Robert Diderich, Chanita D. Kuseva, and Ovanes G. Mekenyan


3. QSAR: What Else? 

Giuseppina Gini


4. (Q)SARs as Adaptations to REACH Information Requirements

Toni Alasuvanto, Andrea Gissi, Tomasz Sobanski, Panagiotis Karamertzanis, and Mike Rasenberg


Part II Molecular and Data Modeling


5. Machine Learning Methods In Computational Toxicology 

Igor I. Baskin


6. Applicability Domain: A Step Toward Confident Predictions And Decidability for QSAR Modeling

Supratik Kar, Kunal Roy, and Jerzy Leszczynski


7. Molecular Similarity In Computational Toxicology

Matteo Floris and Stefania Olla 


8. Molecular Docking for Predictive Toxicology

Daniela Trisciuzzi, Domenico Alberga, Francesco Leonetti, Ettore Novellino, Orazio Nicolotti, and Giuseppe F. Mangiatordi


9. Criteria and Application on the use of Non-Testing Methods within a Weight of Evidence Strategy

Anna Lombardo, Giuseppa Raitano, Domenico Gadaleta, and Emilio Benfenati


10. Characterization and Management of Uncertainties in Toxicological Risk Assessment: Examples from the Opinions of the European Food Safety Authority

Alberto Mantovani


Part III Impact in Drug Discovery and Development


11. Computational Toxicology and Drug Discovery

Catrin Hasselgren and Glenn J. Myatt


12. Approaching Pharmacological Space: Events and Components

Giulio Vistoli, Alessandro Pedretti, Angelica Mazzolari, and Bernard Testa


13. Computational Toxicology Methods in Chemical Library Design and High-Throughput Screening Hit Validation

Kirk E. Hevener


14. Enalos Suite: New Cheminformatics Platform for Drug Discovery and Computational Toxicology 

Dimitra-Danai Varsou, Spyridon Nikolakopoulos, Andreas Tsoumanis, Georgia Melagraki, and Antreas Afantitis


15. Ion Channels In Drug Discovery and Safety Pharmacology 

Paola Imbrici, Orazio Nicolotti, Francesco Leonetti, Diana Conte, and Antonella Liantonio 


16. Computational Approaches in Multi-Target Drug Discovery

Luciana Scotti, Hamilton M. Ishiki, Marcelo Cavalcante Duarte, Tiago Branquinho Oliveira, and Marcus T. Scotti


17. Nano-Formulations for Drug Delivery: Safety, Toxicity, and Efficacy

Antonio Lopalco and Nunzio Denora


18. Toxicity Potential Of Nutraceuticals

Ramesh C. Gupta, Ajay Srivastava, and Rajiv Lall


19. Impact of Pharmaceuticals on the Environment: Risk Assessment using QSAR Modeling Approach

Supratik Kar, Kunal Roy, and Jerzy Leszczynski


Part IV Predicting Human Health Toxicology Endpoints


20. (Q)SAR Methods for Predicting Genotoxicity and Carcinogenicity: Scientific Rationale and Regulatory Frameworks

Cecilia Bossa, Romualdo Benigni, Olga Tcheremenskaia, and Chiara Laura Battistelli


21. Stem Cell-Based Methods to Predict Developmental Chemical Toxicity

Hiroki Takahashi, Xian-Yang Qin, Hideko Sone, and Wataru Fujibuchi


22. Predicting Chemically-Induced Skin Sensitisation by using In Chemico/In Vitro Methods

Laura H. Rossi and Janine Ezendam


23. Hepatotoxicity Prediction by Systems Biology Modeling of Disturbed Metabolic Pathways using Gene Expression Data

Oriol López-Massaguer, Manuel Pastor, Ferran Sanz, and Pablo Carbonell


24. Non-Test Methods to Predict Acute Toxicity: State of Art for Applications of In Silico Methods

Ronan Bureau 


25. Predictive Systems Toxicology

Narsis A. Kiani, Ming-Mei Shang, Hector Zenil, and Jesper Tegner


26. Chemoinformatic Approach to Assess Toxicity of Ionic Liquids

Anita Sosnowska, Anna Rybinska-Fryca, Maciej Barycki, Karolina Jagiello, and Tomasz Puzyn


27. Prediction of Biochemical Endpoints by the CORAL Software: Prejudices, Paradoxes, and Results

Andrey A. Toropov, Alla P. Toropova, Alessandra Roncaglioni, and Emilio Benfenati



Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts