Binding and docking results
Complete the form to generate results.
Energy decomposition
| Component | Complex | Receptor | Ligand | Contribution | Share |
|---|
Reproducible report preview
No report generated.
Formula used
Basic binding energy: ΔEbinding = Ecomplex − Ereceptor − Eligand. Negative values usually indicate favorable association within one consistent protocol. Cross-protocol comparisons require careful normalization and review.
Estimated free energy: ΔGbind = ΔEMM + ΔGsolvation − TΔS + correction. The calculator preserves the signs entered by the user. Confirm each term follows the same convention.
Experimental affinity: ΔG° = RT ln(K), using concentration in molar units. The gas constant is 0.00198720425864 kcal·mol⁻¹·K⁻¹. This conversion is most direct for equilibrium constants.
How to use this calculator
- Select the calculation mode and common output unit.
- Enter energies, docking scores, or affinity measurements.
- Record molecular preparation and docking protocol settings.
- Add residue interactions or batch ligand rows when needed.
- Calculate, inspect warnings, and review the decomposition table.
- Export CSV, JSON, or a printable PDF report.
Example data
| Example | Inputs | Calculation | Result |
|---|---|---|---|
| Basic energy | Complex −1520.80, receptor −1302.35, ligand −205.10 kcal/mol | −1520.80 − (−1302.35) − (−205.10) | −13.35 kcal/mol |
| Free-energy estimate | MM −34.2, solvation 12.8, TΔS 8.4, correction 0 | −34.2 + 12.8 − 8.4 | −29.8 kcal/mol |
| Affinity conversion | Kd 35 nM at 298.15 K | RT ln(35 × 10⁻⁹) | Approximately −10.18 kcal/mol |
Interpretation and limitations
A more negative result often suggests more favorable predicted binding. Near-zero values may indicate weak or uncertain association. Positive values may indicate an unfavorable modeled interaction.
Docking scores are model-dependent ranking quantities. Different scoring functions can use different scales and assumptions. Compare compounds only under a consistent protocol.
High ligand strain can identify unrealistic poses. Poor RMSD may also require manual inspection. Experimental confirmation remains essential for meaningful conclusions.
Frequently asked questions
Does this calculator reproduce MOE results?
No. It analyzes values supplied or exported by users and applies transparent formulas.
Is a docking score the same as binding free energy?
No. A docking score is usually an empirical ranking value, while free energy has thermodynamic meaning.
Should more negative scores always rank first?
Usually for the listed dG-style scores, but users should confirm the selected scoring convention.
Can different scoring functions be compared directly?
Direct comparison is risky because their scales and component weights can differ.
Why does the calculator request preparation settings?
Force fields, protonation, solvation, flexibility, and minimization can materially change results.
What does ligand strain indicate?
Large strain can signal that a pose requires an energetically unfavorable ligand conformation.
Can I convert Kd into free energy?
Yes. The calculator uses ΔG° = RT ln(Kd) after converting Kd into molar units.
Can IC50 be used as Kd?
Not automatically. Assay design and mechanism affect the relationship between these values.
What unit should I use?
Use the unit supplied by your source, then select the desired report unit.
How are batch ligands ranked?
The calculator uses the selected score direction and then binding energy as a secondary value.
What makes confidence low?
Missing protocol details, mixed methods, unminimized structures, incomplete inputs, and warnings reduce confidence.