Protein Analysis

1. 01Molecular weight, isoelectric point and net charge at any pH from the Bjellqvist pKa set, with the terminal corrections applied
2. 02Instability index (Guruprasad 1990) with the published stable-versus-unstable reading stated rather than implied
3. 03GRAVY over any of the twenty-eight ProtParam hydropathy scales, not just Kyte and Doolittle
4. 04Aliphatic index (Ikai 1980) as a thermostability indicator
5. 05Aromaticity (Lobry 1994) and the helix, turn and sheet residue propensities
6. 06Molar extinction coefficient at 280 nanometres for reduced cysteines and for disulfide-bonded cystines, with the corresponding absorbance of a one gram per litre solution
7. 07Windowed hydropathy, hydrophilicity, surface accessibility and flexibility profiles with an adjustable window and edge weight
8. 08Full amino-acid composition as counts and percentages
9. 09Titration curve across the pH range with the isoelectric point marked on it
10. 10Reads the live editor selection or a chosen coding feature, translating in the genetic code you pick, and re-highlights the region on the map
11. 11Non-standard residues and trailing bases outside a whole codon are reported rather than silently dropped
12. 12CSV export of every value, including the composition table and the titration curve

The protein engine ports Biopython ProtParam and is golden-validated byte-for-byte against it across three hundred and sixty-eight assertions, with the aliphatic index validated against the peptides package. The panel runs on @ports/protein.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Why does the composition not add up to one hundred percent?

Because a residue outside the twenty standard amino acids still counts toward the length but has no entry in the composition. This matches ProtParam, and the panel names the residues responsible instead of hiding them.

Which extinction coefficient should I use to read a concentration off an A280?

Use the reduced value when the protein carries free cysteines and the cystine value when disulfide bonds are formed. The panel reports the absorbance of a one gram per litre solution for both, which is the number you divide a reading by.

Can it analyse a coding region rather than a protein sequence?

Yes. Point it at a selection or a coding feature and it translates in the genetic code you choose, stating the frame it used and how many trailing bases fell outside a whole codon.

Why are there twenty-eight hydropathy scales?

Because GRAVY depends on the scale, and a single hardcoded scale would hide that dependence. Every scale ProtParam ships is selectable and each one is validated against the reference implementation.