Hello, I've been attempting to simulate a beta cyclodextrin and drug inclusion complex, where this drug is one that I'm working on for a research project and can act as a ligand. The idea was to have the cyclodextrin act as a receptor to create an inclusion complex, but I haven't been able to achieve this. I have some experience with Autodock4 so I do know that protein-ligand interactions can be simulated with ease. However, I recall reading a post a few days ago that had me thinking if my efforts were for naught. Several commenters claimed the software wasn't viable for simulating these types of interactions. Could anyone please enlighten me on this?
i have not work and idea about cyclodextrin . you mention cyclodextrin as receptor but in docking receptor is protein and cyclodextrin is glucose i.e in category of polysaccharide.
Thus i have no idea but if you done please also share
You would be right, the cyclodextrin is not meant to be a typical receptor but I was wondering if the autodock software by any chance could read it as such. The beta cyclodextrin is used to encapsulate other hydrophobic substances like drugs with such properties. That’s why I was asking this question. If I find anything I’ll let you know too. Thank you for your response either way I appreciate it.
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