Protein Alpha Helix Prediction Calculator

Analyze favorable residues, breakers, charge, and hydrophobic balance. View window scores and confidence notes immediately. Understand sequence regions likely to favor alpha helix formation.

Calculator Input

Paste a raw sequence or FASTA text. Headers and unsupported characters are removed automatically.

Short label for the report and exports.
Residues scored together in each sliding window.
Higher thresholds make predictions stricter.
Penalty per glycine or proline inside a window.
Penalty for helix-opposing beta-branched residues.
Bonus for balanced positive and negative residues.
Rewards common helix capping residues at window ends.
Adds amphipathic helix character to the score.
Shorter covered runs are removed from final output.
Use one-letter amino acid codes only.

Example Data Table

This table uses the built-in sample sequence and default settings.

Example Name Sequence Length Average Propensity Predicted Helix % Longest Stretch Best Window Best Score Verdict
Helix-rich peptide MKALEEKLKALEEKLAALEGGQAL 24 1.289 83.33% 20 LKALEE 1.491 Strong alpha helix tendency

Formula Used

1) Average alpha helix propensity
Average Pα = (Σ residue alpha propensity in window) / window size
2) Window stability score
Score = Average Pα - (breaker penalty × Gly/Pro count) - (I/V/T penalty × I/V/T count) + (salt bonus × salt bridge pairs) + (cap bonus × cap hits) + (hydrophobic moment weight × μH)
3) Hydrophobic moment
μH = sqrt((Σ hᵢ cos θᵢ)² + (Σ hᵢ sin θᵢ)²) / n
The calculator uses 100 degrees per residue for alpha-helical rotation.
4) Final helix coverage
Helix % = (predicted helix residues / total residues) × 100

This model is a rule-based estimator using residue propensities, breaker pressure, salt-pair balance, capping support, and amphipathic character. It is useful for screening and teaching, not for replacing experimental or deep-learning structure pipelines.

How to Use This Calculator

  1. Enter a sequence name for labeling outputs.
  2. Paste your amino acid sequence or FASTA content.
  3. Choose a window size. Six is a practical starting point.
  4. Set the score threshold. Increase it for stricter calling.
  5. Adjust breaker, beta, salt, cap, and hydrophobic weights if needed.
  6. Set the minimum helix run to remove very short fragments.
  7. Press Predict Alpha Helix to display the result above the form.
  8. Review summary metrics, predicted segments, window scores, and residue details.
  9. Download the report as CSV or PDF when needed.

FAQs

1) What does this calculator predict?

It estimates whether local sequence regions are favorable for alpha helix formation. The result is a propensity-based screen, not a solved three-dimensional structure.

2) Is this the same as a full protein structure predictor?

No. This tool is much simpler. It focuses on alpha helix tendency using sequence rules, while full predictors model broader structural context and long-range interactions.

3) Why are glycine and proline penalized?

Both often weaken alpha helices. Proline disrupts backbone geometry, while glycine adds high flexibility that can reduce helical stability in many sequence contexts.

4) Why does the calculator use sliding windows?

Helices form over local sequence segments rather than single residues alone. Sliding windows help detect continuous regions with enough collective support to sustain helical structure.

5) What is the hydrophobic moment used for?

Hydrophobic moment measures amphipathic patterning across a helical face. It helps highlight windows whose residue arrangement supports a structured helical surface.

6) Can this screen membrane helices?

It can provide a rough hint, but membrane helices often need dedicated transmembrane models, stronger hydrophobic analysis, and topology-aware interpretation.

7) Why might a helix-rich sequence still score lower than expected?

Breaker residues, strong beta-branched content, short runs, or a stricter threshold can lower the final score even when several residues have good intrinsic helix propensity.

8) What sequence formats are accepted?

The calculator accepts one-letter amino acid sequences and FASTA text. Unsupported letters, symbols, and numbers are removed before scoring.

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Important Note: All the Calculators listed in this site are for educational purpose only and we do not guarentee the accuracy of results. Please do consult with other sources as well.