Ef Hand Loop Screen

Screen predicted EF-hand loops by length and acidic-residue count.

Description

An EF-hand-loop screen checks segment length and acidic residue count.

An EF-hand-loop screen checks segment length and acidic residue count. Those two features alone provide a limited candidate screen.^[1]

Screen predicted EF-hand loops by length and acidic-residue count.

When to use Ef Hand Loop Screen

Use this tool to screen predicted EF-hand loops by length and acidic-residue count.

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 Ef Hand Loop Screen 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 loopSequence, expectedLength, minimumAcidicResidues using the field table and calculation rules, then run the tool.
Read loopLength, acidicResidueCount, candidate. 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
loopSequence	Loop sequence	string	Required
expectedLength	Expected length	number	Required
minimumAcidicResidues	Minimum acidic residues	number	Required

Enter a canonical loop sequence and finite expected length/minimum count. Count D/E and return length, count and combined flag. The two criteria are not separately constrained to positive integers.

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.

candidate=(loopLength=expectedLength) AND (D/E count≥minimumAcidicResidues)

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

Output field	Meaning	Value type
loopLength	Loop length	number
acidicResidueCount	Acidic residue count	number
candidate	Candidate	boolean

json

{
  "input": {
    "loopSequence": "DADAEGADAEGA",
    "expectedLength": 12,
    "minimumAcidicResidues": 4
  },
  "output": {
    "loopLength": 12,
    "acidicResidueCount": 5,
    "candidate": true
  }
}

Limitations and assumptions

No residue-position pattern, metal coordination, structure or calcium-binding evidence is evaluated.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use C2H2 Zinc Finger Motifs: Find C2H2 zinc-finger cysteine/histidine spacing patterns. For a complementary task, use Homeodomain Length: Check a predicted homeodomain against caller-supplied length bounds.

References

Ef Hand Loop Screen — tool.io

Similar or alternative tools

C2H2 Zinc Finger Motifs
Find C2H2 zinc-finger cysteine/histidine spacing patterns.
Homeodomain Length
Check a predicted homeodomain against caller-supplied length bounds.