This website uses cookies to improve your experience. Read our Privacy Policy
Research articles, tutorials, and practical guidance tagged Ligand Preparation.
Find a method, workflow, scientific concept, or software decision.
Prepare single ligands or SDF libraries for AutoDock Vina with Meeko while preserving chemical identity, state, atom mapping, validation decisions, and provenance.
Read the analysisFilter the publication by research area or keyword.
Evidence-led articles on scientific methods, reproducible workflows, and software decisions.
Learn what a PDBQT file stores, how ligand torsion trees differ from rigid receptor records, why bond orders can be lost, and what to inspect before an AutoDock Vina run.
An SDF file can load and still be unfit for docking. Diagnose valence, aromaticity, fragments, stereochemistry, hydrogens, 3D geometry, minimization, and PDBQT failures before AutoDock Vina.
Prepare receptor and ligand inputs for AutoDock Vina with a reproducible workflow for structure selection, protonation, PDBQT generation, inspection, and preparation records.