Protein Molecular Weight Calculator
Compute molecular weight, isoelectric point, extinction coefficient and composition.
🌐 Runs on the SeqBench API — also callable via REST & MCP, and in bulk from the batch tools
Paste a protein sequence to compute its molecular weight, theoretical isoelectric point (pI), net charge at pH 7, molar extinction coefficient at 280 nm, GRAVY hydropathy and full amino-acid composition. It provides a ProtParam-style readout for designing expression constructs, planning purification, or estimating protein concentration from absorbance.
0 residues · non amino-acid characters are ignored
Values use average residue masses, the EMBOSS pKa set for pI and net charge, and Edelhoch extinction coefficients. Treat them as close estimates — exact figures depend on modifications, buffer and method.
How to use the Protein Properties tool
- 1Paste a protein sequence using one-letter amino-acid codes (FASTA accepted).
- 2Read the molecular weight, theoretical pI, charge and extinction coefficient.
- 3Use ε₂₈₀ and A(0.1%) to convert A280 absorbance into protein concentration.
Frequently asked questions
How is the isoelectric point (pI) calculated?
The pI is the pH at which the protein's net charge is zero. It is found by solving the charge equation with standard side-chain pKa values (the EMBOSS set) plus the N- and C-termini.
How do I use the extinction coefficient?
Divide your measured A280 by the A(0.1%) value to get concentration in mg/mL, or divide by the molar ε₂₈₀ (after accounting for path length) to get molar concentration. We report values for reduced cysteines and for cysteines forming cystines.
Which amino acids are recognised?
The 20 standard amino acids in one-letter code. Other characters (spaces, numbers, ambiguity codes) are ignored so pasted sequences work without cleanup.
Learn more
Related references
One-letter and three-letter amino acid codes with key properties.
Side-chain and terminal pKa values and how they set the isoelectric point.
Common affinity, epitope and solubility protein tags with amino acid sequences, mass, purification/detection and protease cleavage.
Related tools
Digest a protein with trypsin, Lys-C, chymotrypsin and more, and get peptide masses.
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.