Meeko

Ligand preparation toolkit used with AutoDock Vina when formal charges and atom typing must survive conversion into PDBQT.

Why It Matters

Meeko is the safer preparation path when Vina inputs need explicit charge handling. In the STRC docking notes, it appears as the replacement for fragile default Gasteiger workflows that can make anionic ligands look neutral or otherwise distort the ranking axis.

Local Pattern

Use Meeko after a pH-aware protonation step, then inspect the resulting PDBQT charge state before trusting the docking run. The important audit question is not “did Vina finish?”, it is “did the prepared ligand still encode the chemistry being tested?”

Connections

• [applies] Vina Ligand Prep — Gasteiger Zero-Anion Artifact and Dimorphite-Meeko Fix
• [see-also] Vina
• [part-of] Tools