Dear altruist,
I have selected a potential enzyme as a drug target in silico. I have also successfully detected the binding pocket of that desired enzyme. Then I tried the ChimeraX tool to find out pocket coordinates that are required for molecular docking analysis. But unfortunately, I couldn't find them using ChimeraX. So, I am in need of some potential suggestions to find out the pocket coordinates.
Best regards.
Since you have detected the binding pocket of your protein, to find out the pocket coordinates would depend on the software you'll be using for molecular docking proceedings. Every molecular docking tool has a specific way in determining the binding coordinate
Biovia Discovery studio can do that and it's also free, it can find active sites and give you its coordinates which then you can put into the autodock or vina software to perform the molecular docking
MOE site finder and LIGAND SCOUT EXPERT software calculate the active sites.
For drug-related activities, you can also use DoGSiteScorer and PockDrug. These can evaluate the possibility of druggness for the pocket as well as find other pockets. These servers also provide the coordinates.
And for docking purposes, you need to select/assign an area where your ligand should bind that can be selected using ADTools (Autodock tools). There are a few youtube tutorials that explain how to use ADT and Autodock or VINA.
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