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tkella47 / BioChem_DiffDock

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AlphaFold Pre-Work #5

Open iamallrightpie opened 9 months ago

iamallrightpie commented 9 months ago

I'm a little confused about how to use the output from the prework and perform docking and Ligplus with Imatinib for alphafold. I downloaded the zip file from alpha fold and there's 5 different pdbs in there. Are we just supposed to open those files in Ligplus along with the 2hyy pdb? Or do we need to use chimera too?

tkella47 commented 9 months ago

Alphafold generates 5 poses that are its guesses of what is the right structure. This can be necessary in the case where the protein can have different Conformers.

Take the one of these pdbs, and then upload that to the diffdock huggingface space ( and paste the corresponding ligand SMILES)

This will generate the correct position for the ligand.

You then need to merge the protein and ligand models using chimeraX and our python script before opening in LigPlus.

Hope this helps. Reply for any further help

vhjulian commented 9 months ago

Attached is a simple flowchart that explains the input, output, and tool for each step in this process, starting from folding your desired protein in alpha fold.

Hope this helps! AssessmentIIFlowChart.pdf