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Currently accepted at: JMIR Bioinformatics and Biotechnology

Date Submitted: Apr 3, 2019
Date Accepted: Sep 24, 2019

This paper has been accepted and is currently in production.

It will appear shortly on 10.2196/14232

The final accepted version (not copyedited yet) is in this tab.

Warning: This is an author submission that is not peer-reviewed or edited. Preprints - unless they show as "accepted" - should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information.

Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

  • Sania Safdar Butt; 
  • Yasmeen Badshah; 
  • Maria Shabbir; 
  • Mehak Rafiq

In the field of drug discovery, many methods of molecular modeling have been employed to study complex biological and chemical systems. Experimental strategies are integrated with computational approaches for the identification, characterization, and development of novel drugs and compounds. In modern drug designing, molecular docking is an approach that explores the confirmation of a ligand within the binding site of a macromolecule. To date, many software and tools for docking have been employed. AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) is one of the computationally fastest and most accurate software employed in docking. In this paper, a sequential demonstration of molecular docking of the ligand fisetin with the target protein Akt has been provided, using AutoDock Vina in UCSF Chimera 1.12. The first step involves target protein ID retrieval from the protein database, the second step involves visualization of the protein structure in UCSF Chimera, the third step involves preparation of the target protein for docking, the fourth step involves preparation of the ligand for docking, the fifth step involves docking of the ligand and the target protein as Mol.2 files in Chimera by using AutoDock Vina, and the final step involves interpretation and analysis of the docking results. By following the guidelines and steps outlined in this paper, researchers with no previous background in bioinformatics research can perform computational docking in an easier and more user-friendly manner.


Please cite as:

Butt SS, Badshah Y, Shabbir M, Rafiq M

Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

JMIR Preprints. 03/04/2019:14232

DOI: 10.2196/preprints.14232


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