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良い Vina スコアとは？（kcal/mol）
普遍的な閾値はない。相対順位、redock RMSD、ポーズギャップ、誠実な Discussion の書き方。
What is a good Vina score? Short answer: there is no universal cutoff like “−7 kcal/mol = binder.” AutoDock Vina affinity is a relative ranking score inside one receptor, one box, and one preparation protocol — not an experimental ΔG. Markers and TAs fail reports that treat a single number as proof of binding. This page gives defensible rules of thumb for coursework, plus copy-ready Discussion sentences.
What the Vina score actually is
Vina reports affinity in kcal/mol (more negative ≈ stronger predicted binding under the scoring function). It combines steric, hydrophobic, and hydrogen-bond-like terms from a trained empirical function. It does not include explicit solvent entropy, induced-fit protein motion, or experimental Kd. Official docs stress validation on your system with known actives or a native ligand before trusting hits.
- Comparable: analogs docked the same day with the same PDB, box, and pH.
- Not comparable: your −8.1 vs a paper’s −9.4 on a different crystal, different protonation, or different exhaustiveness.
Rules of thumb (use with caveats)
| Affinity (kcal/mol) | Coursework-safe reading | What you must still do |
|---|---|---|
| More positive than −5 | Usually weak / non-binder under typical drug-like boxes | Check box size, protonation, and that the ligand is in the pocket |
| ≈ −6 to −8 | Common “interesting” range for many oral-drug-like ligands | Compare to redocked native ligand; inspect H-bonds |
| More negative than −9 | Strong relative prediction — not automatic hit confirmation | Rule out oversized box artifacts and clashy poses |
| Within 0.5 of another analog | Essentially a tie for ranking | Use interactions / QC, not the third decimal place |
Best practice for a thesis table: report the native ligand redock score (or a known active) as an internal benchmark, then rank your series relative to that number — never cite a magic global cutoff.
When a “good” score is still a bad result
- Pose sits outside the literature pocket (wrong chain / wrong box).
gap_to_second< 0.5 kcal/mol — top modes are ambiguous; show an overlay.- PoseBusters / steric flags fail while affinity looks excellent.
- Every analog scores within 0.2 kcal/mol — you learned nothing about SAR.
Full workflow: interpret affinity, poses, and pose quality.
Discussion sentences you can adapt
“The predicted Vina affinity of −7.4 kcal/mol is more favorable than the vehicle control analog (−5.1 kcal/mol) under identical rigid-receptor settings, but does not constitute experimental proof of binding. Pose quality and PLIP contacts were inspected before ranking.”
“No absolute affinity cutoff was applied; compounds were ranked relative to the co-crystal ligand redock (−8.0 kcal/mol, RMSD X.X Å) prepared with the same Meeko protocol.”
How Dock reports scores
Each ligand gets top poses with affinity, optional redock RMSD, PLIP interactions, and PDF/ZIP tables you can paste into Word. Run a free Review setup first, then dock: AutoDock Vina online.
Related: receptor & ligand prep · thesis Methods templates · common Vina errors.