Molecular Docking of Compounds using Avogadro and AutoDock

The 3D structures of titled compounds were drawn, and energy of each compound was minimized and saved in the pdb format by using Avogadro [28 (link)]. Subsequently, AutoDock Tools 4.2 [29 (link)] was used to open the pdb files, and torque adjustment was made by detecting roots and adjusting as desired. Then, the files were saved in the pdbqt format. Meantime, the structure data format (SDF) structure of the control, lopinavir (CID: 92727), was downloaded from the PubChem database (www.pubchem.ncbi.nlm.nih.gov). The structure data file (SDF) format was subjected to the energy minimization process using MMFF94 (Merck Molecular Force Field 94) force field algorithm [30 (link)], the minimized structure was converted into PDBQT format using PyRx before performing molecular docking analysis.

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Salih R.H., Hasan A.H., Hussein A.J., Samad M.K., Shakya S., Jamalis J., Hawaiz F.E, & Pratama M.R. (2022). One-pot synthesis, molecular docking, ADMET, and DFT studies of novel pyrazolines as promising SARS-CoV-2 main protease inhibitors. Research on Chemical Intermediates, 48(11), 4729-4751.

Publication 2022

AutoDock Tools 4.2 MMFF94

Lopinavir Molecular force Roots Torque

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Variable analysis

independent variables

3D structures of titled compounds
Energy minimization of each compound using Avogadro
Structure of the control, lopinavir (CID: 92727), downloaded from the PubChem database
Energy minimization of the control structure using MMFF94 force field algorithm

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

controls

Positive control: Lopinavir (CID: 92727)
Negative control: Not specified

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