Protein Cleavage Rule Workbench

How to use Protein Cleavage Rule Workbench

Explore a transparent simplified cleavage model with residue coordinates that can be checked against the original sequence. Before/after cut rules and an opposite-side blocking set are supplied directly; no real enzyme specificity is inferred from a familiar example.

1. Enter input, cut residue set, blocked adjacent residue set (opposite side), maximum missed declared cuts (0–3), minimum peptide length, maximum peptide length.
2. Choose the settings for protein cleavage rule workbench, then run the tool.
3. Review the result and any limitations before copying or downloading it.

Good to know

• 10,000 plain ASCII protein letters from the standard 20-letter alphabet plus literal X, no FASTA or whitespace. Rule sets must be distinct supported letters. At most 3 missed cuts; 5,000 output peptides or 300,000 total peptide residues, checked before allocation.
• Explicit simplified boundary rules only. The KR/not-P example is not a complete trypsin model: real exceptions, structure, modifications and experimental conditions are not modeled. X is literal. No medical, diagnostic, proteomics-confidence or experimental-outcome claim.
• Processing is local. Output is limited to 1,000,000 text characters unless a stricter file limit is stated.