Coiled Coil Register
Score coiled-coil heptad register by hydrophobic a/d positions.
Description
Coiled-coil register scoring compares hydrophobic counts at a/d-like positions across seven offsets.
Coiled-coil register scoring compares hydrophobic counts at a/d-like positions across seven offsets. It selects the register with most hits rather than highest normalized fraction.1
Score coiled-coil heptad register by hydrophobic a/d positions.
When to use Coiled Coil Register
Use this tool to score coiled-coil heptad register by hydrophobic a/d positions.
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 Coiled Coil Register 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, hydrophobicResidues using the field table and calculation rules, then run the tool.
- Read bestRegister, hydrophobicCoreCount. 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 |
| hydrophobicResidues | Hydrophobic residues | string | Required |
Enter a canonical sequence and case-sensitive hydrophobic residue-set string. Score registers zero through six and return first best register and raw hydrophobic-core count.
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.
score_r=count(hydrophobic residues with (i−r) mod7 in {0,3}); best=first maximum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| bestRegister | Best register | number |
| hydrophobicCoreCount | Hydrophobic core count | number |
{
"input": {
"sequence": "AALAAALAALAAAL",
"hydrophobicResidues": "AILMVF"
},
"output": {
"bestRegister": 0,
"hydrophobicCoreCount": 4
}
}Limitations and assumptions
Different registers can sample different numbers of positions. No length minimum, normalized score, candidate cutoff or structural prediction is applied.
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 Heptad Hydrophobicity: Score a/d heptad hydrophobicity as a coiled-coil candidate feature. For a complementary task, use Leucine Zipper Pattern: Scan every seventh residue for leucine-zipper runs.
References
-
Coiled Coil Register — tool.io
Similar or alternative tools
- Heptad Hydrophobicity
Score a/d heptad hydrophobicity as a coiled-coil candidate feature.
- Leucine Zipper Pattern
Scan every seventh residue for leucine-zipper runs.