Docking does not begin when the search algorithm starts. It begins when a biological question is translated into a target state, a binding region, a ligand set, and a set of controls.
Define the intended state
Record the organism, construct, cofactors, relevant mutations, experimental conditions, and why the selected structure represents the question. If several structures are plausible, preserve that choice as an explicit branch rather than silently selecting one.
Inspect the protein
Check missing residues and atoms, alternate conformations, unresolved loops, non-standard residues, crystallographic waters, metals, and bound cofactors. Each correction should be recorded with the source file and software version.
Inspect the ligands
Normalize identifiers without discarding the original reference. Review valence, stereochemistry, tautomers, protonation states, formal charges, and three-dimensional conformers. A technically valid file can still encode the wrong chemical species.
Establish controls
Before screening candidates, test whether the protocol can recover a known pose or distinguish known active and inactive compounds where evidence exists. Report failures as part of the method; do not hide them behind a final score table.
The expected output of preparation is not merely a folder of converted files. It is a prepared input set accompanied by a validation record that explains what changed and why.