Hello, My name is Zeta Tamimi from Faculty of Pharmacy University of Indonesia. I am in my 8th semester doing a research about In silico mechanism of some sea cucumber bio active compounds as anti-breast cancer using AutoDock and Vina.
I am having trouble during screening several bioactive compounds that I tested towards 5 target receptors (ER-alpha, FGFR1, IGFR1, PR, VEGFR2) in breast cancer using AutoDock, such as frondoside A, Holothurin A, Intercendensides A-C, okhotoside B1-B3, and 24-dehydroechinoside. All of them contains sulfate group.
There are two problems that are found during screening in AutoDock. First, AutoDock cannot process the screening because the selection molecules page object has no attribute tree (Figure 1). Second of all, I attempt to neutralist the compounds by reducing the sulfate group. The results is the compound shows binding energy except for the okhotoside B2 (Figure 3) and Okhotoside B3 (Figure 4). The AutoDock cannot found any docked conformation in those compounds (Figure 2).
Thank you for your attention and I am looking forward for your respond regarding to this case
- okhotoside B2
- figure 3.jpg (26.43 KiB) Viewed 5413 times
- AutoDock cannot found any docked conformation
- figure 2.jpg (110.3 KiB) Viewed 5413 times
- the selection molecules page object has no attribute tree
- figure 1.jpg (100.47 KiB) Viewed 5413 times