Protein Instability Score

Score protein dipeptide instability with caller-provided empirical weights.

Description

A dipeptide instability proxy combines empirical weights for adjacent residue pairs.

A dipeptide instability proxy combines empirical weights for adjacent residue pairs. Its scale and normalization are caller choices rather than a fixed published index.^[1]

Score protein dipeptide instability with caller-provided empirical weights.

When to use Protein Instability Score

Use this tool to score protein dipeptide instability with caller-provided empirical weights.

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 Protein Instability 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, dipeptideKeys, dipeptideWeights, scaleFactor using the field table and calculation rules, then run the tool.
Read weightedMean, instabilityProxy. 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
dipeptideKeys	Dipeptide keys	list of string	Required
dipeptideWeights	Dipeptide weights	list of number	Required
scaleFactor	Scale factor	number	Required

Enter at least two canonical residues, unique exact dipeptide keys, aligned finite weights and a finite scale factor. Every pair occurring in the sequence must have a supplied weight. Return adjacent-pair mean and scaled proxy.

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.

weightedMean=Σweights(adjacentPair)/(length−1); proxy=weightedMean×scaleFactor

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
weightedMean	Weighted mean	number
instabilityProxy	Instability proxy	number

json

{
  "input": {
    "sequence": "ACD",
    "dipeptideKeys": [
      "AC",
      "CD"
    ],
    "dipeptideWeights": [
      2,
      4
    ],
    "scaleFactor": 10
  },
  "output": {
    "weightedMean": 3,
    "instabilityProxy": 30
  }
}

Limitations and assumptions

Keys are not normalized. This divides by length−1 and uses an arbitrary scale, so it is not automatically the published instability index or a calibrated stability classification.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. 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 Helix Proline Fraction: Measure alpha-helix-disrupting proline fraction.

References

Protein Instability Score — tool.io

Similar or alternative tools

Disorder Residue Fraction
Estimate intrinsic-disorder residue composition using a caller-selected residue set.
Helix Proline Fraction
Measure alpha-helix-disrupting proline fraction.