Peptide solubility calculator
Paste an amino-acid sequence to predict how a research peptide will dissolve. The tool estimates net charge and hydropathy (GRAVY) and recommends a starting solvent using the standard charge-based solubility rule. Free and no sign-up.
How peptide solubility is predicted
Solubility is driven mainly by two properties you can read straight off the sequence: overall charge and hydrophobicity. A charged peptide interacts readily with water; a hydrophobic, uncharged one would rather associate with itself, which is what aggregation is. The classic laboratory rule follows from that — dissolve a peptide in a solvent that maximises its charge, then dilute into your working buffer.
This tool counts the acidic residues (Asp, Glu) and basic residues (Lys, Arg, His) to estimate net charge at physiological pH, and averages the Kyte–Doolittle hydropathy values across the sequence to give a GRAVY score. A positive GRAVY means the peptide is on balance hydrophobic; a negative GRAVY means it is hydrophilic. It then applies the charge-based rule:
- Net negative (≤ −1.5) — dissolve first in a small volume of a basic aqueous buffer (dilute ammonium bicarbonate or ammonia), then dilute with sterile distilled water.
- Net positive (≥ +1.5) — dissolve first in a small volume of dilute (10–30%) acetic acid, then dilute with sterile distilled water.
- Near-neutral and hydrophobic (GRAVY > 0.5) — start with a minimal volume of an organic co-solvent such as DMSO or acetonitrile, then add aqueous diluent slowly.
- Near-neutral and hydrophilic — reconstitute directly with sterile distilled or deionised water.
Reading the result: two worked examples
The 4-residue sequence AEDG contains two acidic residues (E and D) and no basic ones. With the free termini cancelling, that gives a net charge of about −2 and a GRAVY of −1.40 — net-negative and hydrophilic, so the tool recommends a basic buffer first. Its average molecular weight is 390.35 g/mol.
By contrast the sequence TKPRPGP carries two basic residues (K and R) and no acidic ones, giving a net charge of about +2 and a GRAVY of −2.04. Same hydrophilic character, opposite charge — so the recommendation flips to dilute acetic acid. This is the rule doing its job: the sign of the charge, not the size of the peptide, decides the starting solvent.
Practical handling notes
A prediction narrows the search; it does not replace a solubility test. A few points that consistently matter at the bench:
- Test a small aliquot first. Dissolve a few milligrams before committing the whole vial — this is the single cheapest way to avoid losing material to a bad solvent choice.
- Add solvent to peptide, not the reverse, and use the minimum volume that achieves dissolution before diluting to your working concentration.
- Sonication in a water bath helps; vigorous vortexing of a hydrophobic sequence can encourage aggregation instead.
- Keep DMSO to a minimum. If a peptide contains free cysteine or methionine, DMSO can promote oxidation, and residual DMSO may not be compatible with your downstream assay.
- Sequences rich in Ile, Leu, Val, Phe and Trp are the hardest cases. A GRAVY above roughly 1.0 with little charge is a peptide that will fight you.
Once you know the right solvent, use the reconstitution calculator to set the volume, the molarity calculator for concentration, and the molecular weight calculator to confirm the peptide mass.
Hydropathy and charge reference
The values below are exactly what this tool uses. Hydropathy is the Kyte–Doolittle index: strongly positive residues (Ile 4.5, Val 4.2, Leu 3.8) are hydrophobic, strongly negative ones (Arg −4.5, Lys −3.9) are hydrophilic. GRAVY is simply the mean of these values across the sequence.
Average residue masses and Kyte–Doolittle hydropathy values used by this calculator| Code | 3-letter | Amino acid | Residue mass (Da) | Hydropathy (KD) |
|---|
| A | Ala | Alanine | 71.0779 | 1.8 |
| R | Arg | Arginine | 156.1857 | -4.5 |
| N | Asn | Asparagine | 114.1026 | -3.5 |
| D | Asp | Aspartic acid | 115.0874 | -3.5 |
| C | Cys | Cysteine | 103.1429 | 2.5 |
| E | Glu | Glutamic acid | 129.1140 | -3.5 |
| Q | Gln | Glutamine | 128.1292 | -3.5 |
| G | Gly | Glycine | 57.0513 | -0.4 |
| H | His | Histidine | 137.1393 | -3.2 |
| I | Ile | Isoleucine | 113.1576 | 4.5 |
| L | Leu | Leucine | 113.1576 | 3.8 |
| K | Lys | Lysine | 128.1723 | -3.9 |
| M | Met | Methionine | 131.1926 | 1.9 |
| F | Phe | Phenylalanine | 147.1766 | 2.8 |
| P | Pro | Proline | 97.1152 | -1.6 |
| S | Ser | Serine | 87.0773 | -0.8 |
| T | Thr | Threonine | 101.1039 | -0.7 |
| W | Trp | Tryptophan | 186.2099 | -0.9 |
| Y | Tyr | Tyrosine | 163.1733 | -1.3 |
| V | Val | Valine | 99.1311 | 4.2 |
Frequently asked questions
How do you predict whether a peptide will dissolve?
Estimate the net charge from the sequence and pick a solvent that maximises it. Count aspartic and glutamic acid as −1 and lysine and arginine as +1, then add the free termini. A net-negative peptide dissolves best in a basic buffer, a net-positive peptide in dilute acetic acid. If the peptide is near-neutral, the Kyte–Doolittle GRAVY score decides: hydrophobic sequences need an organic co-solvent such as DMSO, hydrophilic ones dissolve directly in water.
What is a GRAVY score?
GRAVY (grand average of hydropathy) is the mean Kyte–Doolittle hydropathy value across all residues in a sequence. A positive GRAVY indicates an overall hydrophobic peptide that is more likely to need an organic co-solvent; a negative GRAVY indicates a hydrophilic peptide that will generally dissolve in aqueous solvent. This calculator reports GRAVY alongside net charge because the two together determine the recommendation.
Why will my peptide not dissolve in water?
Most often the sequence is hydrophobic, near-neutral in charge, or both — there is little for water to interact with. Enter the sequence above to check its net charge and GRAVY. If it is net-charged, a small volume of the matching acidic or basic solvent will usually dissolve it before you dilute with water. If it is near-neutral and hydrophobic, a minimal volume of DMSO is the usual starting point. Sonicating in a water bath also helps.
Should I use acetic acid or ammonium bicarbonate?
It depends on the sign of the net charge. Dilute acetic acid protonates and dissolves net-positive (basic) peptides. Dilute ammonium bicarbonate or ammonia deprotonates and dissolves net-negative (acidic) peptides. Using the wrong one drives the peptide towards its isoelectric point, where solubility is at its minimum.
Is a solubility prediction a guarantee?
No. It is a sequence-based heuristic using net charge and hydropathy, and it does not account for secondary structure, aggregation propensity, modifications, salt form or batch-specific factors. Treat it as a starting point, always test a small aliquot before committing a full vial, and confirm against the manufacturer certificate of analysis.
A predictive guide for in-vitro laboratory research only. Always confirm against the manufacturer's certificate of analysis and handle solvents per your laboratory's safety protocols.
For in-vitro laboratory research use only. Not for human or veterinary use, consumption, or therapeutic application. No medical claims are made.