A Free ProtParam Alternative That Runs in Your Browser
SeqBench's Protein Properties tool computes the ProtParam readout from a pasted sequence — molecular weight, theoretical pI, molar extinction coefficient at 280 nm, GRAVY, aliphatic index, instability index, estimated half-life and full amino-acid composition — with no account and nothing to install.
Three differences worth knowing before you switch: the net charge comes back as a curve across the whole pH range rather than a single pI, the calculation happens in the page rather than on a server, and the same function is callable from a REST API and an MCP server. One thing is missing, and it is in the table below.
SeqBench vs ExPASy ProtParam
| Aspect | SeqBench | ExPASy ProtParam |
|---|---|---|
| Access model | Web app, no account | Web form, no account |
| Price | Free | Free |
| Molecular weight | Yes — average masses, one water added per chain | Yes |
| Theoretical pI | Yes, plus the full net-charge titration curve from pH 0 to 14 at a step you choose | Yes — a single pI value |
| Extinction coefficient | Yes — reduced and all-cystine, each with its A(0.1%) value | Yes — reduced and all-cystine |
| GRAVY hydropathy | Yes, and a windowed Kyte-Doolittle / Hopp-Woods / Eisenberg profile on a separate tool | Yes — one GRAVY value |
| Aliphatic index | Yes | Yes |
| Instability index | Yes, with the stable / unstable call at the published cutoff of 40 | Yes |
| Estimated half-life | Yes — mammalian reticulocytes, yeast and E. coli, from the N-end rule | Yes |
| Amino-acid composition | Yes — counts and percentages for all 20, plus charged-residue totals | Yes |
| Atomic composition | No — we do not report the C/H/N/O/S formula or total atom count | Yes |
| FASTA input | Paste the record with its header; the header's letters are never read as residues | Accepts a raw sequence |
| Several sequences at once | Refused with a reason — a fused chain has a weight, a pI and a half-life that belong to no real protein. The batch endpoint runs a whole multi-FASTA properly | One sequence per submission |
| Where it runs | In your browser — no request leaves the page for this calculation | On the ExPASy server |
| API and AI-agent access | Yes — the same function behind a JSON REST endpoint and an MCP server | No public API |
Comparison is simplified and provided in good faith — check ExPASy for current behaviour. ProtParam is part of the ExPASy server operated by the SIB Swiss Institute of Bioinformatics and is not affiliated with SeqBench.
Where SeqBench is the better fit
- You need the net charge at your buffer's pH, not just the pI
- You would rather the sequence did not leave the browser
- You want the same numbers from a script, a pipeline or an AI agent
- You have a whole FASTA of sequences and want one result per record
- You want the hydropathy profile and the peptide map from the same place
Where ProtParam still wins
- Atomic composition — the C/H/N/O/S formula and total atom count
- Going straight from a UniProt entry with the sub-sequence already selected
- Two decades of being the reference every reviewer recognises
Related protein tools
Compute molecular weight, isoelectric point, extinction coefficient and composition.
Sliding-window hydropathy plot to spot transmembrane and surface regions.
Digest a protein with trypsin, Lys-C, chymotrypsin and more, and get peptide masses.
Back-translate a protein to DNA using most-frequent or degenerate IUPAC codons.
Submit a protein for domain architecture, family and GO-term annotation via EBI InterProScan.
Look up a UniProt accession's AlphaFold prediction, view it in 3D with pLDDT confidence coloring, and highlight residue ranges.
Frequently asked questions
Is there a free alternative to ExPASy ProtParam?
Yes. SeqBench's Protein Properties tool computes the same readout from a pasted sequence — molecular weight, theoretical pI, molar extinction coefficient at 280 nm (reduced and all-cystine), GRAVY, aliphatic index, instability index, estimated half-life and full amino-acid composition — with no account and nothing to install. The one thing ProtParam reports that it does not is the atomic composition formula.
Does it use the same extinction coefficient constants as ProtParam?
Yes — 5,500 M⁻¹cm⁻¹ per tryptophan, 1,490 per tyrosine and 125 per cystine, the values from Pace et al. 1995. Mature hen lysozyme comes out at 37,470 reduced and 37,970 with its four disulfides, which over a molecular weight of 14,313.14 Da gives A(0.1%) values of 2.618 and 2.653 — the second reproducing the commonly quoted literature figure of about 2.64.
What does SeqBench give that ProtParam does not?
Three things. The net charge is reported as a curve across pH 0 to 14 rather than as a single pI, so you can read the charge at your actual buffer pH. The calculation runs in your browser, so the sequence never leaves the page. And the same function is exposed as a JSON REST endpoint and through an MCP server, so a script or an AI agent can call it — ProtParam has no public API.
Can I submit several proteins at once?
Not to the single-sequence tool, and that refusal is deliberate: pasting a multi-record FASTA would concatenate the chains, and the weight, pI, extinction coefficient and half-life of a fused chain belong to a protein nobody has. The tool says so rather than returning a number. For a real set, the batch endpoint runs one tool over a whole multi-FASTA and returns one result per record.
Why do two tools disagree about the same protein's pI?
Because pI is not measured, it is solved for — the pH at which the modelled net charge crosses zero — and the model needs a pKa for every ionisable group plus both termini. Different published pKa sets move the answer by a few tenths of a unit, and some tools also differ on whether to count the terminal groups of a chain they were given as a fragment. The guide on protein molecular weight and pI works through where the disagreement comes from.
Is the instability index a prediction I should act on?
Treat it as a flag, not a verdict. It is a published statistic over dipeptide frequencies with a cutoff at 40, computed from the sequence alone — it knows nothing about your construct's folding, tags, expression host or buffer. A value over 40 is a reason to look at the sequence again, not a reason to expect the protein to fail.