Helix Proline Fraction
Measure alpha-helix-disrupting proline fraction.
Description
Proline fraction summarizes a residue feature relevant to helix-context inspection.
Proline fraction summarizes a residue feature relevant to helix-context inspection. A composition count does not locate or predict helices.1
Measure alpha-helix-disrupting proline fraction.
When to use Helix Proline Fraction
Use this tool to measure alpha-helix-disrupting proline fraction.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Helix Proline Fraction and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter sequence using the field table and calculation rules, then run the tool.
- Read prolineCount, prolineFraction. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| sequence | Sequence | string | Required |
Enter a canonical sequence. Return proline count and fraction in 0–1.
The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.
prolineFraction=Pcount/sequenceLength Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| prolineCount | Proline count | number |
| prolineFraction | Proline fraction | number |
{
"input": {
"sequence": "APPA"
},
"output": {
"prolineCount": 2,
"prolineFraction": 0.5
}
}Limitations and assumptions
No secondary-structure model or position-dependent effect is used. Proline presence does not by itself establish disruption of a particular helix.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Disorder Residue Fraction: Estimate intrinsic-disorder residue composition using a caller-selected residue set. For a complementary task, use Beta Turn Window Score: Rank beta-turn candidate windows by caller-selected turn-favoring residues.
References
-
Helix Proline Fraction — tool.io
Similar or alternative tools
- Disorder Residue Fraction
Estimate intrinsic-disorder residue composition using a caller-selected residue set.
- Beta Turn Window Score
Rank beta-turn candidate windows by caller-selected turn-favoring residues.