Methods | Ligandly
Research methods
Methods before metrics
Protein–ligand computational analysis requires explicit treatment of protein preparation, ligand preparation, search-space definition, scoring assumptions, and validation.
Interpreting predictions
Docking scores are model-dependent estimates, not experimental binding affinities. Structural poses should be assessed against the preparation workflow, plausible contacts, and available experimental evidence.
Reproducibility checklist
Document structure identifiers, software versions, protonation assumptions, docking-box coordinates, random seeds when applicable, and visualization settings.