Number of runs variations on Autodock 4 do not have a significant effect on RMSD from docking results
- Authors: Pratama M.F.1,2, Siswandono S.1
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Affiliations:
- Airlangga University
- Muhammadiyah Palangkaraya University
- Issue: Vol 8, No 6 (2020)
- Pages: 476-480
- Section: Articles
- URL: https://journals.rcsi.science/2307-9266/article/view/111677
- DOI: https://doi.org/10.19163/2307-9266-2020-8-6-476-480
- ID: 111677
Cite item
Abstract
The aim. The number of runs in the docking process with AutoDock 4 is known to play an important role in the validity of the results obtained. The greater the number of runs it is often associated with the more valid docking results. However, it is not known exactly how the most ideal runs in the docking process with AutoDock 4. This study aims to determine the effect of the number of runs docking processes with AutoDock 4 on the validity of the docking results.
Materials and methods. The method used is the redocking process with AutoDock 4.2.6. The receptor used is an estrogen receptor with ligand reference estradiol (PDB ID 1GWR). Variations were made on the number of runs from 10 to 100 in multiples of 10. The parameters observed were RMSD, free energy of binding, inhibition constants, amino acid residues, and the number of hydrogen bonds.
Results. All experiments produce identical bond free energy, where the maximum difference in inhibition constant is only 0.06 nM. The lowest RMSD is indicated by the number of runs of 60, with a RMSD value of 0.942. There is no linear relationship between the number of runs and RMSD, with R in the linear equation of 0.4607.
Conclusion. Overall, the number of runs does not show a significant contribution to the validity of the results of docking with AutoDock 4. However, these results have only been proven with the receptors used.
Keywords
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##article.viewOnOriginalSite##About the authors
Mohammad Rizki Fadhil Pratama
Airlangga University; Muhammadiyah Palangkaraya University
Email: m.rizkifadhil@umpalangkaraya.ac.id
ORCID iD: 0000-0002-0727-4392
Ph.D. student of Pharmaceutical Chemistry from Doctoral Program of Pharmaceutical Sciences; Assistant Professor of Medicinal Chemistry from Department of Pharmacy
Indonesia, Dr. Ir. Soekarno St. Сampus C, Mulyorejo, Surabaya, East Java, Indonesia 60115; RTA Milono St. Km. 1.5, Pahandut, Palangka Raya, Central Kalimantan, Indonesia 73111S. Siswandono
Airlangga University
Author for correspondence.
Email: prof.sis@ff.unair.ac.id
ORCID iD: 0000-0002-9579-8929
Professor of Medicinal Chemistry from Department of Pharmaceutical Chemistry
Indonesia, Dr. Ir. Soekarno St. Сampus C, Mulyorejo, Surabaya, East Java, Indonesia 60115References
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