Protein molecular weight calculator
Calculate protein molecular weight from amino acid sequences in Da and kDa.
Input
Output
Configure input settings on the left, then click "Generate"
Calculate protein molecular weight from amino acid sequences in Da and kDa.
Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.
Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.
Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.
Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.
Calculate the instability index of protein sequences. Values above 40 indicate an unstable protein with a short half-life in vitro.
Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.
Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.
Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.
Faithful static-mode Aggrescan3D tool for per-residue aggregation propensity analysis from a single protein structure.
Plot net charge vs pH for protein sequences. Visualize how protein charge changes across pH 0-14 and identify the isoelectric point (pI) where the net charge crosses zero.
Protein molecular weight is the theoretical mass of a protein chain calculated from its amino acid sequence. It is reported in Daltons (Da) or kilodaltons (kDa), where 1 kDa equals 1,000 Da. Researchers use protein molecular weight to estimate SDS-PAGE band positions, plan purification workflows, compare constructs, and interpret intact-protein mass spectrometry data.
This protein molecular weight calculator converts one or more amino acid sequences into Da and kDa values. It accepts FASTA input, raw one-letter protein sequences, and CSV sequence tables. For a broader sequence-property report that includes pI, extinction coefficients, instability index, aliphatic index, GRAVY, and atomic composition, use Protein Parameters.
The result is theoretical. Signal peptide cleavage, initiator methionine removal, post-translational modifications, disulfide bonds, cofactors, fusion tags, and glycosylation can all make the measured protein mass differ from the value calculated from the primary sequence alone.
The calculator uses amino acid residue masses. Residue masses already account for the water lost during peptide-bond formation, so the neutral protein mass is calculated by adding one terminal water molecule for the N-terminus and C-terminus:
where is the residue mass of each amino acid and is the terminal water mass. The default average water mass is 18.01528 Da. The monoisotopic water mass is 18.01056 Da.
For example, the average-mass calculation for Met-Ala-Gly is:
| Term | Mass (Da) |
|---|---|
| Met residue | 131.1926 |
| Ala residue | 71.0788 |
| Gly residue | 57.0519 |
| Terminal water | 18.01528 |
| Total | 277.33858 |
The calculator reports this sequence as 277.339 Da, or 0.277339 kDa.
| Setting | Default | Effect |
|---|---|---|
| Mass type | Average | Uses average isotope masses for routine protein work. Choose monoisotopic for high-resolution mass spectrometry. |
| Remove initiator Met | No | Removes an N-terminal methionine before calculating mass when the mature protein lacks the initiator residue. |
| Disulfide bonds | 0 | Subtracts the mass of two hydrogens per disulfide bond. Values above the possible cysteine-pair count are clamped. |
The default calculation uses average isotopic residue masses:
| Amino acid | Mass (Da) | Amino acid | Mass (Da) |
|---|---|---|---|
| Ala (A) | 71.08 | Leu (L) | 113.16 |
| Arg (R) | 156.19 | Lys (K) | 128.17 |
| Asn (N) | 114.10 | Met (M) | 131.19 |
| Asp (D) | 115.09 | Phe (F) | 147.18 |
| Cys (C) | 103.14 | Pro (P) | 97.12 |
| Glu (E) | 129.12 | Ser (S) | 87.08 |
| Gln (Q) | 128.13 | Thr (T) | 101.11 |
| Gly (G) | 57.05 | Trp (W) | 186.21 |
| His (H) | 137.14 | Tyr (Y) | 163.18 |
| Ile (I) | 113.16 | Val (V) | 99.13 |
Paste a FASTA record, a raw one-letter amino acid sequence, or a CSV table with a recognizable sequence column such as sequence, seq, or protein. Uploaded files can use .txt, .csv, .fasta, .fa, or .fas.
FASTA input can contain multiple proteins:
>Protein1
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGE
>Protein2
GIVEQCCTSICSLYQLENYCNCSV input is useful when sequence IDs and sequences are already in a spreadsheet:
id,sequence
p1,MAG
p2,ACDBefore submitting, choose the mass type and any correction settings that match the protein you want to calculate. Leave disulfide bonds at 0 for reduced proteins or when the oxidation state is unknown. If a sequence contains ambiguous amino acid codes such as B, Z, J, or X, the calculator reports a warning because those residues require averaged or approximate masses.
Each input sequence produces one row in the results table:
| Column | Meaning |
|---|---|
| Protein ID | The first identifier from the FASTA header or CSV ID column. |
| Amino acids | Sequence length after optional initiator Met removal. |
| Molecular weight (Da) | Calculated protein molecular weight in Daltons. |
| Molecular weight (kDa) | The same value divided by 1,000. |
| Mass type | Average or monoisotopic. |
| Disulfides assumed | Number of disulfide bonds applied after clamping to available cysteine pairs. |
Dalton values are displayed to three decimal places. Kilodalton values are displayed to six decimal places so small peptides and protein-size estimates remain readable in the same table.
For gel electrophoresis, kDa is usually the most convenient unit because protein ladders and apparent band sizes are labeled in kDa. For mass spectrometry and stoichiometry calculations, Da or g/mol values are often more direct; numerically, 1 Da per molecule corresponds to 1 g/mol.
The molecular weight result represents the sequence and settings provided. It does not automatically add glycosylation, phosphorylation, acetylation, lipidation, heme, metals, fluorescent labels, affinity tags, or other modifications. Add those masses separately when they are known.
Disulfide correction only changes the mass by subtracting two hydrogens per bond. It does not predict which cysteines pair or whether a protein is reduced or oxidized under experimental conditions.
For related calculations, use Protein Parameters for a multi-property sequence report, extinction coefficient for A280-based concentration planning, and peptide mass for protease digestion and peptide mass spectrometry workflows.