Open AccessNUMBER OF RUNS VARIATIONS ON AUTODOCK 4 DO NOT HAVE A SIGNIFICANT EFFECT ON RMSD FROM DOCKING RESULTS
Author(s) -
M.P. Ф. Пратама,
C. Сисвандоно
Publication year - 2021
Publication title -
farmaciâ i farmakologiâ
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.174
H-Index - 3
eISSN - 2413-2241
pISSN - 2307-9266
DOI - 10.19163/2307-9266-2020-8-6-476-480
Subject(s) - autodock , docking (animal) , chemistry , hydrogen bond , mathematics , computational chemistry , molecule , veterinary medicine , organic chemistry , biochemistry , in silico , gene , medicine
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.