Analyze biochemical and physical parameters of your protein sequences
Input Protein Sequence
Only standard amino acid characters are accepted.
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Our Protein Half-Life Calculator is a dedicated, web-based tool for predicting the in vivo stability of your protein. By inputting an amino acid sequence, you can instantly receive an estimate of its half-life—the time it takes for half of the protein amount to be degraded within a cell. This prediction is based on the “N-end rule,” which correlates a protein’s lifespan with the identity of its N-terminal amino acid. This tool is invaluable for molecular biologists and biochemists studying protein expression, regulation, and turnover in various model organisms.
How to Use
Analyzing your protein sequence is a simple, three-step process:
- Input Sequence: Paste your protein sequence into the text box. The sequence should contain only standard single-letter amino acid codes.
- Analyze: Click the “Analyze Sequence” button to process your data.
- Review Results: The tool will instantly display a comprehensive report, including the estimated half-life of your protein in three different biological systems.
Tip: For the most relevant half-life prediction, ensure the sequence you provide represents the final, processed form of the protein, as cleavage of a signal peptide can expose a new N-terminal residue.
How is the Protein Half-Life Calculated?
The estimated half-life is calculated based on the N-end rule, a well-established principle in cell biology. This rule states that the identity of the amino acid at the N-terminus of a protein is a primary determinant of its rate of degradation in vivo.
The calculation process is straightforward:
- The tool identifies the first amino acid (the N-terminal residue) of the input sequence.
- It then consults a database of experimentally determined half-lives associated with each of the 20 standard amino acids.
- The tool provides predictions for three different expression systems, as the protein degradation machinery (and thus the N-end rule) varies between organisms:
- Mammalian reticulocytes
- Yeast (Saccharomyces cerevisiae)
- E. coli
For example, a protein starting with Methionine (a “stabilizing” residue) is predicted to have a long half-life (>20 hours in mammals), whereas a protein starting with Arginine (a “destabilizing” residue) is predicted to be degraded rapidly (<2 minutes in E. coli).
Features and Outputs
This protein parameters analyzer provides the following comprehensive outputs:
- Estimated Half-Life: Predicts the protein’s stability and lifespan within different biological systems, offering in-vitro estimates for mammalian reticulocytes, yeast, and E. coli based on the N-end rule.
- Instability Index: Computes a score to predict the protein’s stability in a test tube. A value below 40 suggests a stable protein, while a value above 40 indicates potential instability.
- Amino Acid Composition: Delivers the absolute count and percentage frequency for each of the 20 standard amino acids in your sequence.
- Molecular Weight (MW): Calculates the protein’s molecular weight based on the average isotopic masses of its constituent amino acids.
- Theoretical Isoelectric Point (pI): Estimates the pH at which the protein carries no net electrical charge.
- Amino Acid Property Groups: Classifies and sums amino acids based on their chemical properties (e.g., Hydrophobic, Polar, Positively Charged, Negatively Charged).
- Atomic Composition: Provides the total count of each atom type (Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur) that makes up the protein molecule.
- Extinction Coefficient: Estimates the molar absorption coefficient of the protein at 280 nm, essential for determining protein concentration.
- Aliphatic Index: Calculates the relative volume of the protein occupied by aliphatic side chains, a positive indicator of thermostability.
- Grand Average of Hydropathicity (GRAVY): A score representing the overall hydrophobicity of the protein.
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FAQ
References & Suggested Reading
This tool was developed in line with established principles in computational biochemistry for accurate, reliable results. The resources listed below are the foundational research and key papers that define these standards, and we highly recommend them for a deeper understanding of the scientific principles.
- Bachmair, A., Finley, D., & Varshavsky, A. (1986). In vivo half-life of a protein is a function of its amino-terminal residue. Science, 234(4773), 179–186. https://doi.org/10.1126/science.3018930
- Varshavsky, A. (2011). The N-end rule pathway and regulation of apoptosis. Nature Cell Biology, 13(9), 1024–1026. https://doi.org/10.1038/ncb2326
- Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In J. M. Walker (Ed.), The Proteomics Protocols Handbook (pp. 571–607). Humana Press. https://doi.org/10.1385/1-59259-890-0:571
Meet the Authors
Mahdi Morshedi Yekta
Founder & Bioinformatics Developer
Mahdi is the founder of ScienceCodons and a Medical Biotechnologist with a deep passion for computational biology. Holding an M.Sc. in Medical Biotechnology, he specializes in transforming complex biological algorithms into accessible, high-performance web tools, bridging the gap between laboratory sciences and software engineering.
Fatemeh Faryadras
Medical Biotechnologist & Researcher
Fatemeh is a Medical Biotechnologist and researcher. With extensive expertise in genetic engineering, molecular cloning, and cancer biology, she combines her rigorous laboratory background with intuitive design principles to create reliable, user-centered scientific calculators and tools.
Dr. Mosayeb Rostamian
Assistant Professor, Infectious Diseases Research Center
Certified Scientific Reviewer
Google ScholarExpert Review Process
To ensure the highest quality and scientific accuracy, this tool's underlying algorithms, formulas, and edge-case handling have been thoroughly reviewed and validated by Dr. Mosayeb Rostamian.
The "Reviewed By" badge signifies that an independent expert has evaluated the tool's logic to guarantee accuracy and alignment with the current consensus in the scientific community.