Protein Calculators | MW, pI & A280 Concentration

Protein analysis tools

Every tool below opens instantly and runs entirely in your browser — nothing is uploaded, stored or logged.

Protein Molecular Weight CalculatorCalculate protein molecular weight in Da and kDa from an amino-acid sequence, with the full residue-mass table, composition counts and Da↔mg/mL↔µM bridges.
Protein Isoelectric Point (pI) CalculatorCalculate a protein isoelectric point (pI) from its sequence using the EMBOSS pKa set, with net charge at pH 7 and a charge-vs-pH curve.
Protein Concentration Calculator (A280)Convert an A280 reading to protein concentration in mg/mL and µM — derive ε280 from the sequence (Trp/Tyr/Cys) or enter it, with path length and dilution.

Once you have a purified protein or a cloned sequence, three numbers come up again and again: how heavy it is, what pH it stops moving in a field, and how much of it is actually in the tube. These are sequence-and-spectroscopy calculations, not nutrition estimates — this collection is for the molecular biology and biochemistry bench. Each tool shows the chemistry behind the answer, works through real numbers, and cites where the constants come from. Everything runs locally in your browser, so a sequence you paste is never uploaded.

Molecular Weight from a Sequence

A protein’s mass is the sum of its residue masses plus one water molecule. Each amino acid contributes its residue mass — the free amino acid minus the water lost when the peptide bond formed — so the protein molecular weight calculator adds the 20 standard residue masses (plus selenocysteine and pyrrolysine if present), then adds back 18.0153 Da for the terminal OH and H. It returns the mass in Da and kDa, the per-residue composition, and the two conversion factors you need downstream: µg per nmol and nmol per µg. Leave the sequence blank and give a length instead and it falls back to the ~110 Da average-residue estimate, clearly flagged as approximate. The how to calculate protein molecular weight guide explains why you sum residues and not free amino acids, and how the average estimate differs from the exact one.

Isoelectric Point and Net Charge

The isoelectric point is the pH at which a protein carries no net charge — the point it stops migrating in an electric field, which is why it governs isoelectric focusing, ion-exchange chromatography and solubility. The protein isoelectric point calculator treats every ionizable group (N- and C-termini plus K, R, H, D, E, C, Y) with the Henderson–Hasselbalch equation, sums the fractional charges, and bisects to the pH where the total crosses zero. Alongside pI it reports the net charge at pH 7, the count of each ionizable residue and a charge-versus-pH curve from 0 to 14. It uses the EMBOSS pKa set, so a theoretical pI can differ from an experimental one by a few tenths — that pKa-set dependence is real, not an error. The how to calculate protein isoelectric point guide covers the charge math, why predicted and measured pI diverge, and how to choose a buffer pH relative to pI.

Concentration from A280

Proteins absorb at 280 nm because of their tryptophan, tyrosine and cystine residues, and the Beer–Lambert law turns that absorbance into a concentration. The protein concentration calculator builds the molar extinction coefficient ε280 straight from the sequence — 5500 per Trp, 1490 per Tyr and 125 per cystine (oxidized cysteine pair) — or takes a measured ε280 directly if you have one. From an A280 reading, path length and dilution factor it returns the molar concentration, and with the molecular weight it converts to mg/mL and gives A(1%, 1 cm). It flags the sequence with no aromatic residues, where A280 quantitation fails and a colorimetric assay is the right call. The how to determine protein concentration from A280 guide works through the ε-from-sequence method, the reduced versus oxidized cysteine choice, and when to use Bradford or BCA instead.

Which calculator do I need?

Start from the number you are missing:

A sequence and you need its mass → protein molecular weight calculator for exact Da/kDa, residue composition and µg-per-nmol.
You need a buffer pH, an IEF position or a chromatography starting point → protein isoelectric point calculator for pI, net charge at pH 7 and the charge curve.
An A280 reading and you need the concentration → protein concentration calculator for mg/mL or µM from a sequence- or measurement-derived ε280.
A dry mass or a molar target once you know the MW → the molarity calculator to go from mass to molar concentration.
You need to dilute a concentrated stock to a working concentration → the dilution calculator or C1V1 calculator.
You are working from nucleic acid rather than protein sequence → the DNA & RNA calculators for DNA molecular weight and A260 concentration.

These tools chain the way a purification does: get the exact mass from the sequence, predict the pI to pick a chromatography or focusing condition, then measure A280 to quantify what you recovered — and carry the molecular weight into the concentration step so an absorbance becomes a mg/mL you can use. For solution prep downstream, hand off to the laboratory calculators.

Protein Analysis Tools

Protein Molecular Weight Calculator — exact mass in Da/kDa from a sequence using standard residue masses plus water, with composition and µg-per-nmol conversions.
Protein Isoelectric Point Calculator — theoretical pI from the EMBOSS pKa set, net charge at pH 7 and a full charge-versus-pH curve.
Protein Concentration Calculator — A280 to mg/mL or µM via the Beer–Lambert law, with ε280 from sequence or measurement.

Frequently asked questions

How is a protein’s molecular weight calculated from its sequence?

By summing the residue mass of each amino acid and adding one water molecule (18.0153 Da). A residue mass is the free amino acid minus the water lost when its peptide bond formed, so the chain is built from residues and the terminal H and OH are added back as a single water. For a sequence with no aromatic surprises this gives the exact monoisotopic-averaged mass; the ~110 Da-per-residue rule of thumb is only an average-composition estimate.

What does the isoelectric point (pI) tell you?

The pI is the pH at which a protein carries zero net charge. Below it the protein is net positive, above it net negative, and at it the protein neither migrates in an electric field nor is well solvated — which is why pI drives isoelectric focusing, ion-exchange chromatography and precipitation. A theoretical pI from pKa values can differ from a measured one by a few tenths of a pH unit.

How does an A280 measurement give protein concentration?

Through the Beer–Lambert law, c = A / (ε × path length). Tryptophan, tyrosine and cystine absorb at 280 nm, so the molar extinction coefficient ε280 is built from the sequence: 5500 M⁻¹cm⁻¹ per Trp, 1490 per Tyr and 125 per cystine. With the absorbance, path length and dilution factor you get a molar concentration, and with the molecular weight you convert it to mg/mL.

When should I use Bradford or BCA instead of A280?

When the protein has few or no aromatic residues (ε280 near zero), when the sample is a crude mixture of many proteins, or when buffers, nucleic acids or reducing agents contaminate the 280 nm reading. A280 is fast and non-destructive for a pure, aromatic-containing protein; colorimetric assays are more robust for impure or aromatic-poor samples but need a standard curve and consume the sample.

Do these calculators store or upload my protein sequence?

No. Every calculation runs locally in your browser. The sequence you paste is never sent to a server, stored or logged, and there is no login.

Protein Analysis Calculators