ProtParam (Expasy): Compute Protein Properties from a Sequence

ProtParam is a web tool on Expasy, the resource portal operated by the SIB Swiss Institute of Bioinformatics, that computes physical and chemical parameters from a protein sequence or a UniProtKB entry. You paste a sequence or enter an accession and get molecular weight, theoretical pI, composition, extinction coefficient, estimated half-life, instability index, aliphatic index and GRAVY. Every value is calculated from the sequence alone, so none of it is a measurement. This guide maps each output to its formula and the limit the documentation states for it. Documentation checked 2026-11-07.

What ProtParam is used for in research

ProtParam answers sequence-level planning questions: roughly what mass and charge behaviour to expect, how to convert a 280 nm absorbance reading into a concentration, and whether a construct looks hydrophobic or compositionally unusual. For converting a concentration between mg/mL and µM once you have the molecular weight, see the protein molarity calculator guide.

Install or access (official source only)

ProtParam is a web server; nothing is installed. It is listed on the Expasy ProtParam resource page and runs at web.expasy.org/protparam. Documentation is at web.expasy.org/protparam/protparam-doc.html. Expasy publishes terms of use at expasy.org/terms-of-use.

Step-by-step: compute parameters for one protein

1. Open web.expasy.org/protparam/. The form is headed “Enter a protein sequence”.
2. Enter either one UniProtKB accession or ID (the form’s examples are P05130 and KPC1_DROME) or one protein sequence in single-letter code. In a raw sequence, spaces and numbers are ignored.
3. If you entered a UniProtKB entry, an intermediate page lets you choose a mature chain, peptide or domain from the feature table, or type custom start and end positions. Leaving the boxes empty analyses the full sequence.
4. Submit the form and read the results page (next section).

Output and how to read it

Each output has a defined formula. The table follows the ProtParam documentation.

Output	How it is computed	How to read it, and the documented caveat
Molecular weight and theoretical pI	Calculated as in the Compute pI/Mw tool	Sequence-based values; post-translational modifications cannot be specified.
Amino acid and atomic composition	Counts from the sequence	Shows the residues (Trp, Tyr, Cys) that drive the extinction coefficient.
Extinction coefficient	E(Prot) = Numb(Tyr)×Ext(Tyr) + Numb(Trp)×Ext(Trp) + Numb(Cystine)×Ext(Cystine), in water at 280 nm, with Ext(Tyr) = 1490, Ext(Trp) = 5500, Ext(Cystine) = 125. Absorbance is E(Prot) divided by molecular weight.	Two values are reported: one assuming all Cys form cystines, one assuming all Cys are reduced. Documented as quite reliable for proteins containing Trp; for proteins without Trp the page notes there may be more than 10% error. Proteins with other chromophores, such as prosthetic groups, cannot be analysed this way.
Estimated half-life	N-end rule; predictions for mammalian (human), yeast and E. coli	Predicted time for half of the protein in a cell to disappear after synthesis. The page calls it an estimation and says it does not apply to N-terminally modified proteins.
Instability index	II = (10/L) × Sum of DIWV(x[i]x[i+1]), L = sequence length	Below 40 predicts a stable protein; above 40 suggests it may be unstable. The threshold rests on a small training set (12 unstable and 32 stable proteins).
Aliphatic index	X(Ala) + 2.9 × X(Val) + 3.9 × (X(Ile) + X(Leu)), with X as mole percent	The relative volume occupied by aliphatic side chains.
GRAVY	Sum of Kyte-Doolittle hydropathy values divided by the number of residues	A single average hydropathy score for the whole sequence.

ProtParam and Expasy

Expasy is the portal; ProtParam is one tool hosted on it. A search for “ProtParam Expasy” is looking for the same page.

Protein molecular weight in kDa and isoelectric point

The molecular weight is reported in daltons; divide by 1000 for kDa. The pI is the theoretical value from the sequence. For how pI is separated experimentally see isoelectric focusing, and for how mass is read from a gel see SDS-PAGE.

Troubleshooting

• Oligomers. ProtParam does not know whether a mature protein forms dimers or multimers. For a known dimer, the documentation suggests duplicating the sequence.
• Modified proteins. Post-translational modifications cannot be specified, so values describe the unmodified sequence.
• Wrong region analysed. To analyse a mature chain rather than a precursor, use the UniProtKB route and pick the chain on the intermediate page, or paste the exact residues.
• Protein with no Trp. Treat the extinction coefficient as less certain; the page notes possible error above 10%.
• Cofactor-bound proteins. Other chromophores absorbing at 280 nm cannot be handled by the extinction calculation.

Free alternatives and related Expasy tool

Tool	Input	What it gives
ProtParam	One UniProtKB AC/ID or one sequence	Mw, pI, composition, extinction coefficient, half-life, instability index, aliphatic index, GRAVY
Compute pI/Mw (Expasy)	One or more UniProtKB accessions/IDs (one per line), one sequence, or an uploaded file	Theoretical pI and Mw, with an average or monoisotopic resolution option

Frequently asked questions

What does ProtParam calculate?

Molecular weight, theoretical pI, amino acid and atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and GRAVY, all from sequence (Expasy ProtParam documentation, checked 2026-11-07).

Can I enter a UniProt accession?

Yes. The form accepts one UniProtKB accession or ID, such as P05130, and lets you choose a mature chain, peptide, domain or custom start and end. To see how a sequence folds, the AlphaFold Protein Structure Database guide covers UniProt-keyed structure predictions; for measuring a protein concentration experimentally, see BCA protein assay and standard curve calculation.

Can ProtParam handle modified proteins or complexes?

No modifications can be specified, and oligomeric state is not inferred; duplicate the sequence for a known dimer.

How do I cite ProtParam?

The Expasy documentation points to: Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The Proteomics Protocols Handbook. Humana Press; 2005. pp 571-607. doi:10.1385/1-59259-890-0:571.

Sources

• ProtParam documentation, Expasy / SIB, checked 2026-11-07
• ProtParam tool page, checked 2026-11-07
• Expasy resource page for ProtParam, checked 2026-11-07
• Compute pI/Mw, checked 2026-11-07