Beta Turn Window Score
Rank beta-turn candidate windows by caller-selected turn-favoring residues.
Description
A beta-turn window proxy measures the proportion of caller-selected residues in local windows.
A beta-turn window proxy measures the proportion of caller-selected residues in local windows. It ranks a composition feature rather than modeling turn geometry.1
Rank beta-turn candidate windows by caller-selected turn-favoring residues.
When to use Beta Turn Window Score
Use this tool to rank beta-turn candidate windows by caller-selected turn-favoring residues.
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 Beta Turn Window Score 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, windowLength, turnResidues using the field table and calculation rules, then run the tool.
- Read windowScores, bestStart. 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 |
| windowLength | Window length | number | Required |
| turnResidues | Turn residues | string | Required |
Enter canonical sequence, positive safe-integer window no longer than it and case-sensitive turn-residue set. Return all window fractions in start order and zero-based first best start.
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.
score_i=selectedResidueCount(window_i)/windowLength; bestStart=first maximum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| windowScores | Window scores | list of number |
| bestStart | Best start | number |
{
"input": {
"sequence": "GPNS",
"windowLength": 4,
"turnResidues": "GPNS"
},
"output": {
"windowScores": [
1
],
"bestStart": 0
}
}Limitations and assumptions
No embedded propensity table, positional weights or secondary-structure validation is used. An empty set gives all-zero scores and best start zero.
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 Helix Proline Fraction: Measure alpha-helix-disrupting proline fraction. For a complementary task, use Disorder Residue Fraction: Estimate intrinsic-disorder residue composition using a caller-selected residue set.
References
-
Beta Turn Window Score — tool.io
Similar or alternative tools
- Helix Proline Fraction
Measure alpha-helix-disrupting proline fraction.
- Disorder Residue Fraction
Estimate intrinsic-disorder residue composition using a caller-selected residue set.