8 An Overview of National Toxicology Program’s Toxicogenomic
Applications: DrugMatrix and ToxFX . . . . . . . . . . . . . . . . . . . . . . 141
Daniel L. Svoboda, Trey Saddler and Scott S. Auerbach
9 A Pair Ranking (PRank) Method for Assessing Assay
Transferability Among the Toxicogenomics Testing Systems . . . . . 159
Zhichao Liu, Brian Delavan, Liyuan Zhu, Ruth Robert
and Weida Tong
10 Applications of Molecular Dynamics Simulations
in Computational Toxicology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Sugunadevi Sakkiah, Rebecca Kusko, Weida Tong and Huixiao Hong
Part II Applications in Regulatory Science
11 Applicability Domain: Towards a More Formal Framework
to Express the Applicability of a Model and the Confidence
in Individual Predictions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Thierry Hanser, Chris Barber, Sébastien Guesné,
Jean François Marchaland and Stéphane Werner
12 Application of Computational Methods for the Safety Assessment
of Food Ingredients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Patra Volarath, Yu (Janet) Zang and Shruti V. Kabadi
13 Predicting the Risks of Drug-Induced Liver Injury in Humans
Utilizing Computational Modeling . . . . . . . . . . . . . . . . . . . . . . . . . 259
Minjun Chen, Jieqiang Zhu, Kristin Ashby, Leihong Wu,
Zhichao Liu, Ping Gong, Chaoyang (Joe) Zhang, Jürgen Borlak,
Huixiao Hong and Weida Tong
14 Predictive Modeling of Tox21 Data . . . . . . . . . . . . . . . . . . . . . . . . . 279
Ruili Huang
15 In Silico Prediction of the Point of Departure (POD)
with High-Throughput Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Dong Wang
16 Molecular Modeling Method Applications: Probing
the Mechanism of Endocrine Disruptor Action . . . . . . . . . . . . . . . . 315
Xianhai Yang, Huihui Liu and Rebecca Kusko
17 Xenobiotic Metabolism by Cytochrome P450 Enzymes:
Insights Gained from Molecular Simulations . . . . . . . . . . . . . . . . . 337
Zhiqiang Fu and Jingwen Chen
x
Contents
Applications: DrugMatrix and ToxFX . . . . . . . . . . . . . . . . . . . . . . 141
Daniel L. Svoboda, Trey Saddler and Scott S. Auerbach
9 A Pair Ranking (PRank) Method for Assessing Assay
Transferability Among the Toxicogenomics Testing Systems . . . . . 159
Zhichao Liu, Brian Delavan, Liyuan Zhu, Ruth Robert
and Weida Tong
10 Applications of Molecular Dynamics Simulations
in Computational Toxicology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Sugunadevi Sakkiah, Rebecca Kusko, Weida Tong and Huixiao Hong
Part II Applications in Regulatory Science
11 Applicability Domain: Towards a More Formal Framework
to Express the Applicability of a Model and the Confidence
in Individual Predictions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Thierry Hanser, Chris Barber, Sébastien Guesné,
Jean François Marchaland and Stéphane Werner
12 Application of Computational Methods for the Safety Assessment
of Food Ingredients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Patra Volarath, Yu (Janet) Zang and Shruti V. Kabadi
13 Predicting the Risks of Drug-Induced Liver Injury in Humans
Utilizing Computational Modeling . . . . . . . . . . . . . . . . . . . . . . . . . 259
Minjun Chen, Jieqiang Zhu, Kristin Ashby, Leihong Wu,
Zhichao Liu, Ping Gong, Chaoyang (Joe) Zhang, Jürgen Borlak,
Huixiao Hong and Weida Tong
14 Predictive Modeling of Tox21 Data . . . . . . . . . . . . . . . . . . . . . . . . . 279
Ruili Huang
15 In Silico Prediction of the Point of Departure (POD)
with High-Throughput Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Dong Wang
16 Molecular Modeling Method Applications: Probing
the Mechanism of Endocrine Disruptor Action . . . . . . . . . . . . . . . . 315
Xianhai Yang, Huihui Liu and Rebecca Kusko
17 Xenobiotic Metabolism by Cytochrome P450 Enzymes:
Insights Gained from Molecular Simulations . . . . . . . . . . . . . . . . . 337
Zhiqiang Fu and Jingwen Chen
x
Contents