Calculator inputs
Example data table
| Sample | Length | Window | Alpha helix % | Beta sheet % | Turn % | Coil % | Dominant state |
|---|---|---|---|---|---|---|---|
| Albumin fragment A | 44 | 6 | 38.64 | 20.45 | 11.36 | 29.55 | Alpha helix |
| Beta-rich motif B | 30 | 5 | 16.67 | 43.33 | 10.00 | 30.00 | Beta sheet |
Formula used
1. Windowed propensity averages
For residue position i, the calculator averages Chou–Fasman style residue propensities across a sliding window.
HelixScore(i) = Σ Pα(j) / n
SheetScore(i) = Σ Pβ(j) / n
TurnScore(i) = [Σ Pt(j) / n] × TurnWeight
2. Coil estimate
Coil is treated as a fallback state when ordered structure scores are weaker than the chosen thresholds.
CoilScore(i) = max(0.25, CoilBias + 1.35 − max(HelixScore, SheetScore, TurnScore))
3. State assignment
The dominant structured state must exceed its threshold and also beat the coil score. Otherwise, the residue is assigned as coil.
State(i) = argmax(H, E, T) if score ≥ threshold and score > CoilScore; else Coil
4. Structure percentages
Each class percentage equals assigned residues in that class divided by total sequence length, multiplied by 100.
How to use this calculator
- Enter a sample name to label the report and exports.
- Paste a sequence using standard one-letter amino acid codes.
- Set the window size. Larger windows smooth local fluctuations.
- Adjust helix, sheet, and turn thresholds for stricter classification.
- Use turn weight to emphasize loop-prone residues when needed.
- Use coil bias to make unordered assignments easier or harder.
- Set a minimum segment length for practical motif highlighting.
- Submit the form and review percentages, segments, and residue scores.
FAQs
1. What does this calculator predict?
It estimates whether each residue is more likely to belong to an alpha helix, beta sheet, turn, or coil region using sequence-based propensity values and user-defined thresholds.
2. Is this equivalent to experimental structure assignment?
No. It is a fast heuristic model for sequence screening. Crystal structures, cryo-EM, NMR, DSSP assignments, and circular dichroism remain more reliable for final structural interpretation.
3. Why do the thresholds matter?
Thresholds control how easily helix, sheet, or turn labels are assigned. Higher values reduce false positives but can increase coil predictions in borderline regions.
4. What is the role of window size?
Window size smooths local residue behavior. Smaller windows react quickly to single residues, while larger windows emphasize broader structural tendencies across neighboring positions.
5. Why is there a coil bias input?
Coil bias shifts the fallback score for unordered structure. Raising it makes coil assignments more common when helix, sheet, and turn signals are weak or conflicting.
6. Can I use long protein sequences?
Yes. The calculator can process long sequences, but very large proteins will produce bigger residue tables and larger export files, which may feel heavier in a browser.
7. What does the confidence value mean?
Confidence expresses how strongly the winning state score dominates the combined local scores at that residue. It is a comparative indicator, not a calibrated probability.
8. Why might a known helix appear as coil here?
Short motifs, unusual residue mixtures, strict thresholds, or high coil bias can suppress ordered predictions. Lowering thresholds or reducing coil bias may recover weak structured segments.