Calculator Inputs
Choose a workflow, enter the available experimental or thermodynamic values, and calculate standardized affinity outputs, energy terms, occupancy, and optional ligand efficiency estimates.
Example Data Table
These sample values illustrate how different workflows convert experimental affinity or thermodynamic data into a comparable free energy view.
| Case | Workflow | Primary input | Temperature | Approx. output |
|---|---|---|---|---|
| Fragment screen hit | Kd → ΔG° | Kd = 420 µM | 25 °C | ΔG° ≈ -4.60 kcal/mol, pKd ≈ 3.38 |
| Optimized inhibitor | Ki → ΔG° | Ki = 38 nM | 25 °C | ΔG° ≈ -10.11 kcal/mol, strong affinity |
| Enzyme assay correction | IC50 → Ki → ΔG° | IC50 = 95 nM, [S] = 5 µM, Km = 10 µM | 25 °C | Ki ≈ 63.3 nM, ΔG° ≈ -9.82 kcal/mol |
| ITC thermodynamic profile | ΔH and ΔS → ΔG° | ΔH = -14.2 kcal/mol, ΔS = -18 cal/mol·K | 25 °C | ΔG° ≈ -8.84 kcal/mol, Kd ≈ 330 nM |
Formula Used
1. Standard free energy from dissociation constant:
ΔG° = RT ln(Kd)
2. Standard free energy from association constant:
ΔG° = -RT ln(Ka)
3. Cheng–Prusoff correction for competitive inhibition:
Ki = IC50 / (1 + [S]/Km)
4. Thermodynamic relationship:
ΔG = ΔH - TΔS
5. Reverse conversion from free energy to dissociation constant:
Kd = exp(ΔG° / RT)
6. Fractional occupancy estimate:
θ = [L] / ([L] + Kd)
7. Ligand efficiency estimate:
LE = -ΔG° / heavy atom count
Constants and conventions:
R = 0.0019872043 kcal/mol·K, temperature is converted to Kelvin, and concentration values are standardized to molar units before calculation.
How to Use This Calculator
Step 1: Choose the workflow matching your data source, such as Kd, Ki, IC50, thermodynamic terms, or reverse free-energy conversion.
Step 2: Enter temperature and its unit. The calculator converts Celsius to Kelvin automatically for all thermodynamic equations.
Step 3: Fill only the fields needed for your selected workflow. Hidden sections are ignored during calculation.
Step 4: Add ligand concentration to estimate receptor occupancy and heavy atom count to estimate ligand efficiency.
Step 5: Submit the form. The result panel appears directly below the page header and above the form.
Step 6: Review Kd, Ka, ΔG°, pKd, qualitative affinity, and any corrected or derived terms produced by the selected workflow.
Step 7: Use the export buttons to save a CSV summary or a PDF snapshot of the result section.
FAQs
1. What does this calculator estimate?
It estimates standard protein–ligand binding free energy and related affinity metrics from Kd, Ka, Ki, IC50 assay data, thermodynamic terms, or known ΔG values.
2. Why does the calculator convert everything to molar units?
Thermodynamic affinity equations are standard-state equations. Converting concentrations to molar units keeps Kd, Ki, IC50-derived Ki, and occupancy results internally consistent.
3. When should I use the IC50 workflow?
Use it when inhibition experiments report IC50 instead of Ki or Kd. The calculator applies the Cheng–Prusoff correction using substrate concentration and Km.
4. What does a more negative ΔG mean?
A more negative binding free energy usually indicates more favorable binding under the assumed conditions. It often corresponds to lower Kd and higher affinity.
5. Why is temperature important here?
Temperature affects the RT term in equilibrium conversions and the TΔS term in thermodynamic calculations. Even moderate temperature changes can shift the estimated ΔG or Kd.
6. Is Kd always the same as Ki?
No. They describe related but different quantities. This calculator treats Ki as an affinity-like constant when users need comparable free-energy estimates.
7. What is ligand efficiency?
Ligand efficiency normalizes binding strength by heavy atom count. It helps compare compounds of different sizes during fragment growth or lead optimization.
8. Can I use these outputs as final experimental proof?
No. They are computational interpretations of supplied values. Final conclusions still depend on assay design, standard-state assumptions, experimental uncertainty, and model suitability.