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Let's Dock: A Smart Platform for Molecular Docking

Author(s)
Yaruq Jabeen Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Nida Ansari Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Haroon Rasheed Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Muhammad Asif Rasheed Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Muhammad Awais Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
Muhammad Ibrahim Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Sumaira Kanwal Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Aqsa Khalid National University of Sciences and Technology, H-12, Islamabad, Pakistan
Manzoor Ahmad Zahid Department of Mathematics, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Farrukh Jamil Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab, Pakistan
Abstract
In the past few years, several docking tools have been developed for molecular dockings such as LeDock, rDock, AutoDock Vina, AutoDock, UCSF DOCK, GOLD, Glide, Surflex-Dock, LigandFit and MOEDock. Among these, AutoDock Vina has been widely used by academia for molecular docking. This tool performs docking of a ligand into a protein by seven steps. For docking analysis of several ligands, AutoDock Vina is a time-consuming tool. In order to make AutoDock Vina more eficient and smart way, a platform has been developed in this study. It is designated “Let's Dock”. By using this platform, we can perform a docking analysis of several ligands into a protein with AutoDock Vina by just submitting ligands and protein pdb files. Apart from thermodynamic data analysis this platform also calculates descriptors and Lipinski's rule parameters (Rule of Five) of a ligand by a single click.
Publication Details
Page(s) 1577-1582
DOI 10.17582/journal.pjz/20210109170113
Published Journal: Pakistan Journal of Zoology, Volume: 54, Issue: 4, Year: 2022

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Keywords
molecular docking, AutoDock Vina, Lipinski rule, Virtual screening
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