molecular docking
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9 weeks ago
晓雯 ▴ 20

Guys, I have a problem with already knowing the receptor and the professor gave a model of four ligands. Should I choose the best ligand to bind to the receptor and if so, is the best ligand the one with the least energy drawn with Avigadro?

(hope you can give me some advice on this busy Monday afternoon. Thank you very much for your replies and for reading)

docking • 232 views
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I somehow feel your professor is asking a bit too much from you to just provide you with the files but no prior lessons. We had at least a 3-day course on molecular docking prior to solving some class exercises with the Amber Suite and Dock. However, this was more than 10 years ago, and I remember barely anything but the name of the tools we used.

Maybe this tutorial helps? Some of the file names and commands ring a bell...so it seems to be vaguely similar to the approach we used in the course.

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Yes I thought so too, the professor only gave me a 10 page tutorial to go through. But still, it was a hard thing to finish

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Thank you so much for your reply, I'm off to try it out now. Have a happy day.

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