PDZ Terminal Motif

Classify the terminal tripeptide of a candidate PDZ-binding ligand.

Description

A terminal PDZ-motif classifier inspects the last three residues for two explicit classes.

A terminal PDZ-motif classifier inspects the last three residues for two explicit classes. Residue-pattern classification does not establish interaction with a PDZ domain.^[1]

Classify the terminal tripeptide of a candidate PDZ-binding ligand.

When to use PDZ Terminal Motif

Use this tool to classify the terminal tripeptide of a candidate PDZ-binding ligand.

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 PDZ Terminal Motif 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 terminalTrimer, motifClass. 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 the final three residues, or the whole shorter sequence, and exact pattern class; sequences shorter than three cannot match.

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.

class-I=[ST]-X-[VIL]; class-II=[VILF]-X-[VIL]; otherwise unmatched

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

Output field	Meaning	Value type
terminalTrimer	Terminal trimer	string
motifClass	Motif class	string

json

{
  "input": {
    "sequence": "ASAV"
  },
  "output": {
    "terminalTrimer": "SAV",
    "motifClass": "class-I"
  }
}

Limitations and assumptions

Only these two patterns are tested. Other PDZ preferences, accessibility and binding evidence are not assessed.

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 PTS1 Terminal Signal: Check a peroxisomal PTS1 terminus against caller-accepted tripeptides. For a complementary task, use KDEL Retention Signal: Detect a C-terminal KDEL ER retention signal.

References

PDZ Terminal Motif — tool.io

Similar or alternative tools

PTS1 Terminal Signal
Check a peroxisomal PTS1 terminus against caller-accepted tripeptides.
KDEL Retention Signal
Detect a C-terminal KDEL ER retention signal.