Chymotrypsin Cleavage

Locate aromatic chymotrypsin cleavage sites with optional proline blocking.

Description

A chymotrypsin site screen applies an aromatic-residue rule with optional blocking before proline.

A chymotrypsin site screen applies an aromatic-residue rule with optional blocking before proline. The boolean option controls that explicit boundary condition.^[1]

Locate aromatic chymotrypsin cleavage sites with optional proline blocking.

When to use Chymotrypsin Cleavage

Use this tool to locate aromatic chymotrypsin cleavage sites with optional proline blocking.

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 Chymotrypsin Cleavage 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, blockBeforeProline using the field table and calculation rules, then run the tool.
Read cleavagePositions, cleavageCount. 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
blockBeforeProline	Block before proline	boolean	Required

Enter a canonical sequence and blocking option. Return ascending exclusive cut positions and count, excluding terminal residues as internal boundaries.

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.

cut after internal F/Y/W unless blockBeforeProline AND next=P

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

Output field	Meaning	Value type
cleavagePositions	Cleavage positions	list of number
cleavageCount	Cleavage count	number

json

{
  "input": {
    "sequence": "AFAYWPA",
    "blockBeforeProline": true
  },
  "output": {
    "cleavagePositions": [
      2,
      4
    ],
    "cleavageCount": 2
  }
}

Limitations and assumptions

This is a simplified specificity model without digestion conditions, modifications or measured yield.

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 GLUC Cleavage: Locate Glu-C acidic-residue cleavage sites with a caller Asp option. For a complementary task, use Protease Digest: Simulate sequence digestion from caller-specified cut and blocking residues.

References

Chymotrypsin Cleavage — tool.io

Similar or alternative tools

GLUC Cleavage
Locate Glu-C acidic-residue cleavage sites with a caller Asp option.
Protease Digest
Simulate sequence digestion from caller-specified cut and blocking residues.