ADL: PDB preparation best practices for Vina?

Rick Sheridan ricksher at gmail.com
Tue Dec 15 03:13:31 PST 2020


Hello -

Does anyone know of a preferred go-to reference checklist for preparing a
protein from the PDB for docking in Vina?  For example it might include
steps like 'remove any ligands the model is already in complex with' or
'determine if any solvent molecules are part of the protein's structure' or
managing polar vs non-polar hydrogens.

Best,
Rick

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Rick Sheridan
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