Compute Mw & pI
Students prepping SDS-PAGE routinely google “expected protein Mw” to predict band positions — Bioinformatics.org’s calculator is still a top hit, while ExPASy ProtParam is the gold standard for full physicochemical profiling. This lightweight wizard recreates the two most-wanted outputs — theoretical molecular weight (sum of monoisotopic residue masses) and isoelectric point (Bjellqvist algorithm) – in a single card that runs entirely in your browser, safeguarding proprietary sequences.
- Who it’s for — undergraduates learning SDS-PAGE sizing :contentReference[oaicite:3]{index=3}, diagnostic labs needing Mw for Western-blot marker choice, and bio-hackathon teams verifying tag fusions.
- What it does — cleans raw or FASTA input, counts residues, sums masses, iterates pH 0–14 to find net charge ≈ 0 using standard pKₐ tables.
- Why it helps — predicts gel mobility, informs buffer pH, and flags unlikely sequences (extreme Mw/pI) before expensive synthesis.
Teaching SDS-PAGE – students plot log Mw vs. migration; a quick Mw read-out lets them predict bands before running the gel.
Protein tag planning – adding a 6×His tag (840 Da) or GST (26 kDa) shifts Mw and sometimes the pI; designers can test both instantly.
Buffer optimisation – pI guides buffer pH for IEX or solubility screens ; having Mw & pI side-by-side echoes the ExPASy ProtParam report.
Fully private – runs offline like Bioinformatics.org’s SMS CGI but without server calls, aligning with data-sovereignty best practice.
Who is it for ?
Students & teaching labs
First-year courses that introduce SDS-PAGE need a quick way for students to predict where a band should run; hand-calculating sums for 200-residue proteins is a non-starter.
Bench scientists & CRO cloning cores
Technicians planning Western blots or SEC fractions must know the expected Mw after every tag or fusion is added.
Protein-production & purification teams
The pI guides buffer choice for ion-exchange or IEF; working near the pI often crashes solubility, so flags appear long before precious reagents are wasted.
Bio-hackathon & iGEM teams
Rapid design cycles mean dozens of constructs a day; a browser-only widget eliminates sign-ups and protects IP.
What the calculator does & how it works
- Residue tally – strips non-AA characters, counts each letter, then adds monoisotopic masses plus one H₂O for the termini to give Mw, the same equation taught in Biochemistry 101.
- pI by net-charge balancing – applies Bjellqvist side-chain and terminal pKₐ values, computing the net charge at successive pH points until it crosses zero.
- Fast, private, offline – no CGI or API calls (unlike early ExPASy Perl scripts); results appear in milliseconds and proprietary sequences never leave the laptop.
Why it’s useful
| Lab task | Calculator benefit |
|---|---|
| Predicting SDS-PAGE mobility | Mw tells students which ladder band should match their protein before the gel ever runs. |
| Choosing affinity tags | Shows the 26 kDa GST tag or 840 Da 6×His bump so gels aren’t mis-read. |
| Optimising buffer pH | Working > 1 pH unit away from the pI maximises solubility and prevents precipitation. |
| Troubleshooting unexpected bands | A Mw mismatch flags proteolysis or frame shifts before sequencing results arrive. |
| Budget-friendly classrooms | Eliminates the need for paid software in teaching labs; a Chromebook + browser is enough. |