Maintenance Notice

Due to necessary scheduled maintenance, the JMIR Publications website will be unavailable from Monday, March 11, 2019 at 4:00 PM to 4:30 PM EST. We apologize in advance for any inconvenience this may cause you.

Who will be affected?


Currently submitted to: JMIR Bioinformatics and Biotechnology

Date Submitted: Apr 3, 2019
Open Peer Review Period: Apr 8, 2019 - Jun 3, 2019
(closed for review but you can still tweet)

NOTE: This is an unreviewed Preprint

Warning: This is a unreviewed preprint (What is a preprint?). Readers are warned that the document has not been peer-reviewed by expert/patient reviewers or an academic editor, may contain misleading claims, and is likely to undergo changes before final publication, if accepted, or may have been rejected/withdrawn (a note “no longer under consideration” will appear above).

Peer-review me: Readers with interest and expertise are encouraged to sign up as peer-reviewer, if the paper is within an open peer-review period (in this case, a “Peer-Review Me” button to sign up as reviewer is displayed above). All preprints currently open for review are listed here. Outside of the formal open peer-review period we encourage you to tweet about the preprint.

Citation: Please cite this preprint only for review purposes or for grant applications and CVs (if you are the author).

Final version: If our system detects a final peer-reviewed “version of record” (VoR) published in any journal, a link to that VoR will appear below. Readers are then encourage to cite the VoR instead of this preprint.

Settings: If you are the author, you can login and change the preprint display settings, but the preprint URL/DOI is supposed to be stable and citable, so it should not be removed once posted.

Submit: To post your own preprint, simply submit to any JMIR journal, and choose the appropriate settings to expose your submitted version as preprint.

Click by Click Molecular Docking for non-bioinformaticians using Chimera 1.12

  • 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 the complex biological and chemical systems. Experimental strategies are integrated with computational approaches in the identification, characterization and development of novel drugs and compounds. Molecular Docking is the approach in the modern drug design that explores the confirmation of ligand within the binding site of the macromolecule. To date many software’s and tools for Docking have been employed. AutoDock Vina (in UCSF Chimera) is one of the computationally fast and accurate software employed in Docking. In this paper, a sequential demonstration of molecular Docking of ligand Fisetin with the target protein Akt has been provided, using AutoDock Vina in UCSF Chimera 1.12. The first step involves the target protein ID retrieval from PDB, the second step is to visualize the structure of protein in UCSF Chimera, the third step is to prepare the target protein for Docking, the fourth step is preparing the ligand for docking, the fifth step is the Docking of ligand and the target protein as Mol.2 files in Chimera using AutoDock Vina and the final step is the interpretation and analysis of Docking results. By following the guidelines and the steps used in this paper, the researchers who have no previous background in bioinformatics research can perform computational Docking in a more user-friendly and easy manner.


Please cite as:

Butt SS, Badshah Y, Shabbir M, Rafiq M

Click by Click Molecular Docking for non-bioinformaticians using Chimera 1.12

JMIR Preprints. 03/04/2019:14232

DOI: 10.2196/preprints.14232


Request queued. Please wait while the file is being generated. It may take some time.

© The authors. All rights reserved. This is a privileged document currently under peer-review/community review (or an accepted/rejected manuscript). Authors have provided JMIR Publications with an exclusive license to publish this preprint on it's website for review and ahead-of-print citation purposes only. While the final peer-reviewed paper may be licensed under a cc-by license on publication, at this stage authors and publisher expressively prohibit redistribution of this draft paper other than for review purposes.