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Abbreviations
AFP
α-fetoprotein
AMBER
Assisted Model Building with Energy Refinement
AR
Androgen receptor
CHARMM Chemistry at HARvard Macromolecular Mechanics
DPPC
Dipalmitoylphosphatidylcholine
EDCs
Endocrine disrupting chemicals
GROMACS GROningen MAchine for Chemical Simulations
IFD
Induced fit docking
LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator
MD
Molecular dynamics
NAMD
NAnoscale Molecular Dynamics
NPT
Constant number (N), pressure (P), and temperature (T)
NVE
Constant number (N), volume (V), and energy (E)
NVT
Constant number (N), volume (V), and temperature (T)
nAChRs
Neuronal acetylcholine receptor
PDB
Protein Data Bank
Pmemd
Particle Mesh Ewald Molecular Dynamics
QSAR
Quantitative structure–activity relationship
RMSD
Root-mean-square deviation
RMSF
Root-mean-square fluctuation
SPC
Simple point-charge water model
VMD
Visual molecular dynamics
WT
Wild type
10.1 Introduction
Toxicans are defined as any chemical substance or a mixture of various chemical
substances which completely or partially damages an organism. The toxicity of a
compound or substance is dose-dependent. A toxic chemical entering the human
body is absorbed and interacts with other chemical substances already present in the
body, leading to harm. A driving imperative in the toxicology field is twofold: (1)
Determine the toxic dosage level of compounds, and (2) identify their effects on the
environment and living organisms such as animals, plants, and humans. Both experimental toxicology and computational toxicology predict the toxicity and dosage of
chemicals. Experimental toxicology leverages in vivo and in vitro methods. In vivo
methods are slow to yield compound toxicity predictions (http://alttox.org/mapp/
toxicity-testing-overview Accessed March 19, 2018). The utility of in vitro methods
is constrained by time and cost. Computational toxicology, also known as “in silico
toxicology,” generates predictive models via computation to understand the interactions and adverse health effects of various chemicals present in the air, food, water,
S. Sakkiah et al.
Abbreviations
AFP
α-fetoprotein
AMBER
Assisted Model Building with Energy Refinement
AR
Androgen receptor
CHARMM Chemistry at HARvard Macromolecular Mechanics
DPPC
Dipalmitoylphosphatidylcholine
EDCs
Endocrine disrupting chemicals
GROMACS GROningen MAchine for Chemical Simulations
IFD
Induced fit docking
LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator
MD
Molecular dynamics
NAMD
NAnoscale Molecular Dynamics
NPT
Constant number (N), pressure (P), and temperature (T)
NVE
Constant number (N), volume (V), and energy (E)
NVT
Constant number (N), volume (V), and temperature (T)
nAChRs
Neuronal acetylcholine receptor
PDB
Protein Data Bank
Pmemd
Particle Mesh Ewald Molecular Dynamics
QSAR
Quantitative structure–activity relationship
RMSD
Root-mean-square deviation
RMSF
Root-mean-square fluctuation
SPC
Simple point-charge water model
VMD
Visual molecular dynamics
WT
Wild type
10.1 Introduction
Toxicans are defined as any chemical substance or a mixture of various chemical
substances which completely or partially damages an organism. The toxicity of a
compound or substance is dose-dependent. A toxic chemical entering the human
body is absorbed and interacts with other chemical substances already present in the
body, leading to harm. A driving imperative in the toxicology field is twofold: (1)
Determine the toxic dosage level of compounds, and (2) identify their effects on the
environment and living organisms such as animals, plants, and humans. Both experimental toxicology and computational toxicology predict the toxicity and dosage of
chemicals. Experimental toxicology leverages in vivo and in vitro methods. In vivo
methods are slow to yield compound toxicity predictions (http://alttox.org/mapp/
toxicity-testing-overview Accessed March 19, 2018). The utility of in vitro methods
is constrained by time and cost. Computational toxicology, also known as “in silico
toxicology,” generates predictive models via computation to understand the interactions and adverse health effects of various chemicals present in the air, food, water,