Cleavage Site Calculator
Predict Cleavage Sites in Your Protein Sequence
About the Cleavage Site Calculator
The Cleavage Site Calculator is a free, accurate, and scientifically validated online tool that instantly predicts proteolytic cleavage sites in any protein sequence using established, peer-reviewed specificity rules of over 15 major proteases and chemical cleavage agents. This calculator strictly follows the exact biochemical rules used in proteomics laboratories worldwide and published in high-impact journals.
What is Proteolytic Cleavage and Why is it Important?
Proteolytic cleavage is the hydrolysis of peptide bonds by proteases or chemical agents. Accurate prediction of cleavage sites is essential in:
- Bottom-up proteomics and peptide mapping
- Protein sequencing and mass spectrometry sample preparation
- Recombinant protein purification (cleavable tags)
- Understanding post-translational processing (signal peptides, pro-peptides)
- Drug design targeting protease-substrate interactions
- Studying viral polyprotein processing (HIV, SARS-CoV, etc.)
Scientific Foundation & References
All cleavage rules implemented in this Cleavage Site Calculator are directly taken from peer-reviewed sources including:
- Keil, B. (1992). Specificity of Proteolysis. Springer-Verlag.
- Rawlings et al. (continuously updated). MEROPS peptidase database.
- Nielsen et al. (2016). SignalP 5.0 for signal peptide prediction.
- Duckert et al. (2004). Prediction of proprotein convertase cleavage sites.
Most Commonly Used Cleavage Rules in This Tool
| Agent | Cleavage Rule | Typical Use |
|---|---|---|
| Trypsin | After K or R (not before P) | Gold standard in proteomics |
| Chymotrypsin | After F, Y, W (not before P) | Large hydrophobic residues |
| Cyanogen Bromide | After M (chemical) | 100% specificity |
| TEV Protease | ENLYFQ↓G/S | Recombinant protein tags |
| Furin | R-X-[R/K]-R↓ | Proprotein processing |
When Should You Use the Cleavage Site Calculator?
Use this tool when you need to:
- Design mass spectrometry experiments and predict peptide masses
- Plan digestion protocols for protein identification
- Remove affinity tags from recombinant proteins
- Predict viral polyprotein maturation sites
- Study hormone and neuropeptide processing
- Teach proteomics and biochemistry courses
User Guidelines
- Paste your protein sequence using single-letter amino acid codes (numbers/spaces automatically removed).
- Select the desired protease or chemical agent from the dropdown.
- Optionally check “Show peptide fragments” and “Highlight sites”.
- Click “Predict Cleavage Sites” – results appear instantly.
- Cleavage sites are marked with ↓ and numbered fragments are listed below.
This powerful Cleavage Site Calculator is proudly brought to you by Agri Care Hub. For in-depth scientific review on protease specificity, see the comprehensive study: Cleavage Site analysis in Genomics, Proteomics & Bioinformatics.
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