Applications of Molecular Dynamics Simulations in Computational Toxicology

Abstract

Computational toxicology is a discipline seeking to computationally model and predict toxicity of chemicals including drugs, food additives, and other environmental chemicals. Risk assessment of chemicals using current in vitro or in vivo experimental methods is at best time-consuming and expensive. Computational toxicology seeks to accelerate this process and decrease the cost by predicting the risk of chemicals to humans and animals. Molecular dynamics (MD) simulation, an emerging computational toxicology technique, characterizes the interactions of chemicals with biomolecules such as proteins and nucleic acids. This chapter will give a brief review both of available software tools for MD simulations and also how to apply these software tools to computational toxicology challenges. We also summarize key protocols to run MD simulations.