Protein Sequence Isoelectric Point

Estimate sequence isoelectric pH by bisection of caller-parameterized charge.

Description

Sequence isoelectric pH is a modeled pH where net charge approaches zero.

Sequence isoelectric pH is a modeled pH where net charge approaches zero. The result depends on caller-provided terminal and side-chain pKa values.^[1]

Estimate sequence isoelectric pH by bisection of caller-parameterized charge.

When to use Protein Sequence Isoelectric Point

Use this tool to estimate sequence isoelectric pH by bisection of caller-parameterized charge.

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 Sequence Isoelectric Point 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, pkas, iterations using the field table and calculation rules, then run the tool.
Read isoelectricPh, residualCharge. 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
pkas	Pkas	list of number	Required
iterations	Iterations	number	Required

Enter a canonical sequence, nine finite pKas and a safe-integer iteration count from 1 through 100. Order pKas as N terminus, C terminus, K, R, H, D, E, C, Y. Move the lower bound when charge is positive and upper otherwise; stop early at absolute charge below 1e−12.

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.

bisect pH interval [0,14] using netCharge(pH); residual=netCharge(final pH)

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

Output field	Meaning	Value type
isoelectricPh	Isoelectric ph	number
residualCharge	Residual charge	number

json

{
  "input": {
    "sequence": "A",
    "pkas": [
      7,
      7,
      10,
      12,
      6,
      4,
      4,
      8,
      10
    ],
    "iterations": 32
  },
  "output": {
    "isoelectricPh": 7,
    "residualCharge": 0
  }
}

Limitations and assumptions

The solver does not check that a root is bracketed inside 0–14. Inspect residualCharge, especially for extreme pKas. Modifications and environmental pKa shifts are not inferred.

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 Protein Charge At PH: Estimate sequence net charge at pH from caller-supplied terminal and side-chain pKas. For a complementary task, use Protein Average Mass: Sum average isotopic residue masses plus terminal water for a protein sequence.

References

Protein Sequence Isoelectric Point — tool.io

Similar or alternative tools

Protein Charge At PH
Estimate sequence net charge at pH from caller-supplied terminal and side-chain pKas.
Protein Average Mass
Sum average isotopic residue masses plus terminal water for a protein sequence.