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).