WW Ppxy Motifs

Find PP-X-Y WW-domain ligand candidates.

Description

A WW-domain ligand sequence screen locates candidates with a particular residue pattern.

A WW-domain ligand sequence screen locates candidates with a particular residue pattern. Pattern presence is a starting point for examining biological context and experimental evidence.^[1]

Find PP-X-Y WW-domain ligand candidates.

When to use WW Ppxy Motifs

Use this tool to find PP-X-Y WW-domain ligand candidates.

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 WW Ppxy Motifs 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 ligandStarts, ligandCount. 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 the canonical sequence. Examine each possible start for PP-X-Y, implemented by PP.Y. X means any accepted amino acid. Return zero-based start positions and their count in ascending order; overlapping matches are retained. Only complete windows are tested.

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.

match pattern: PP-X-Y; count=number of matching start positions

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

Output field	Meaning	Value type
ligandStarts	Ligand starts	list of number
ligandCount	Ligand count	number

json

{
  "input": {
    "sequence": "PPAY"
  },
  "output": {
    "ligandStarts": [
      0
    ],
    "ligandCount": 1
  }
}

Limitations and assumptions

The scan is limited to this exact pattern. It does not confirm WW-domain ligand function, structural accessibility or experimental support.

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 SH3 Pxxp Motifs: Locate proline-X-X-proline SH3 ligand motifs. For a complementary task, use Sumoylation Motifs: Find hydrophobic-K-X-E SUMOylation consensus candidates.

References

WW Ppxy Motifs — tool.io

Similar or alternative tools

SH3 Pxxp Motifs
Locate proline-X-X-proline SH3 ligand motifs.
Sumoylation Motifs
Find hydrophobic-K-X-E SUMOylation consensus candidates.