2. Materials and Methods
Conduction of the present in silico study has been made possible
by the assistance of several databases including PubChem
(https://pubchem.ncbi.nlm.nih.gov/), RCSB Protein Data Bank
(https://www.rcsb.org/) and Proteins Plus Server
(https://proteins.plus/); and softwares like Argus lab
(http://www.arguslab.com/arguslab.com/ArgusLab.html), Molinspiration
(https://www.molinspiration.com/), Open Babel (http://openbabel.org),
Hex (http://hex.loria.fr/), and Toxicity Estimation Software Tool
(https://www.epa.gov/chemical-research/toxicity-estimation-software-tool-test).
PubChem is an open chemistry database that provides two-dimensional
chemical information about the ligands being used in this study
(Butkiewicz et al., 2013). The RCSB Protein Data Bank is a global
archive of three-dimensional structural data of biomolecules, per say
viral receptors in this study (Rose et al., 2015). Proteins Plus server
is a common online server for computational drug modeling, wherein one
of its counterparts, namely, Pose View is used to visualize receptor
structures and create pose depictions of ligand-receptor binding.
Moreover, another counterpart of Proteins Plus server, namely, DoG Site
Scorer is used to predict the active binding sites and druggability of
binding pockets of receptors (Fährrolfes et al., 2017; Volkamer et al.,
2012). Argus lab is molecular modeling software which is mainly used to
visualize the receptors as well as ligands and customize both of them
for docking (Joy et al., 2006). Molinspiration is online
chemiinformatics software focused on calculating the molecular
properties of ligands and predicting their bioactivity properties
(Jarrahpour et al., 2012). OpenBabel is an open platform for
inter-converting chemical file formats, thereby aiding in converting the
2D structure of ligands to 3D pdb structure and hence customizing them
for molecular docking (Samdani & Vetrivel, 2018). Hex is an interactive
molecular docking program for calculating the binding energies of
interaction between receptors and ligands (Ritchie & Venkatraman,
2010). Toxicity Estimation Software Tool is a Quantitative Structure
Activity Relationships (QSAR) which is used to estimate the toxicity of
ligands based on the molecular descriptors of the ligands (Barron et
al., 2012).