Input Receptor and Ligand Files FORMATTING Inquiry

[Joel Subach]

Hello for the above topic, can anybody please provide a specific example?

I have a membrane protein receptor bound to a ligand from the pdb but am not sure if I should input
the membrane protein minus the ligand coordinates and moreover am not sure similarly how i should input
the ligand (for example just the bare chemical ligand from pubchem)?

Thanks:)
Joel

[Jacob Durrant]

Hi Joel. The receptor should only include the protein itself. DeepFrag provides an "Automatically remove all protein atoms?" link you can use if your protein does include a ligand.

The ligand file is separate but must represent the ligand in the receptor-bound pose. DeepFrag isn’t a docking program, so it can’t position the ligand for you. But if the ligand is positioned in the bound conformation, DeepFrag can recommend fragment additions.

This tutorial might be helpful: https://www.youtube.com/playlist?list=PLR7O6-it-8SOpQTV8oSVHMg8-_R_4gZRV

Take care,

Jacob

[Author]

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