keep key amino acid residues when docking about autodock-vina HOT 2 OPEN

Hi @TVect
In addition to what Diogo suggested, if you already have a reference protein-ligand structure, you could do restrained conformer generation for the analogs to ensure their core structures align with your reference ligand (well enough for FEP calculations). The confromers can be ranked in Vina by a single-point score calculation (--score_only) or perform a local search (--local_only ) if you don't mind them move a little bit.

from autodock-vina.

Hello,
In same cases, defining a smaller search space that restricts molecules to part of the binding pocket can help, even though this is not a general solution.

A more general solution is what we call "anchored docking" in autodock-gpu (not possible in vina unfortunately). You would define a SMARTS pattern and pin one or more atoms to some coordinates: https://github.com/ccsb-scripps/AutoDock-GPU/wiki/Anchored-docking

from autodock-vina.