protein_properties
Read-only
Molecular weight (average + monoisotopic), molecular formula, isoelectric point, instability index and amphipathicity (Boman index, Eisenberg hydrophobic moment) of a protein sequence (Biopython ProtParam + peptides + pyteomics).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pH | No | pH the net charge is reported at (default 7.0). | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| protein | Yes | the protein sequence (unambiguous one-letter codes); wire it from translate_sequence. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| gravyScale | No | hydropathy scale GRAVY is averaged over (all 28 ProtParam/ProtScale scales; default Kyte & Doolittle). Values: KyteDoolitle (Kyte & Doolittle (1982)), Aboderin (Aboderin (Int J Biochem 2:537)), AbrahamLeo (Abraham & Leo (1987)), Argos (Argos (Eur J Biochem 128:565)), BlackMould (Black & Mould (1991)), BullBreese (Bull & Breese (1974)), Casari (Casari & Sippl, hydrophobic potential (JMB 224:725)), Cid (Cid (Protein Eng 5:373)), Cowan3.4 (Cowan at pH 3.4 (1990)), Cowan7.5 (Cowan at pH 7.5 (1990)), Eisenberg (Eisenberg, normalized consensus (1984)), Engelman (Engelman, transfer free energy (Annu Rev Biophys 15:321)), Fasman (Fasman (1989)), Fauchere (Fauchere (1983)), GoldSack (Goldsack & Chalifoux, free energy of mixing (J Theor Biol 39:645)), Guy (Guy, transfer free energy kcal/mol (1985)), Jones (Jones (J Theor Biol 50:167)), Juretic (Juretic (Theor Comput Chem 5:405)), Kidera (Kidera factors (J Protein Chem 4:23)), Miyazawa (Miyazawa, contact energy from 3D structures (1985)), Parker (Parker, HYDROPHILICITY from HPLC retention (1986)), Ponnuswamy (Ponnuswamy, folded-protein character (Prog Biophys Mol Biol 59:57)), Rose (Rose (1985)), Roseman (Roseman (1988)), Sweet (Sweet, optimized matching OMH (1983)), Tanford (Tanford (1962)), Wilson (Wilson, hydrophobic constants from HPLC retention (1981)), Zimmerman (Zimmerman (J Theor Biol 21:170)). | KyteDoolitle |
| momentWindow | No | sliding window for the hydrophobic moment, in residues (default 11; clamped to the sequence length). | |
| cystineConvention | No | how the oxidised e280 counts cysteines: 'cystine' = 125 per disulfide (ProtParam, default) or 'perCysteine' = 62.5 per residue (SnapGene). They differ only on an ODD cysteine count. | cystine |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mw | Yes | molecular weight [Da] — a FLOOR when `nonStandard` is non-empty, because ProtParam has no mass for those letters and still counts them in the length | |
| pI | Yes | isoelectric point | |
| a280 | Yes | A280 of a 1 g/L solution (cystines form) — divide a spectrophotometer reading by this | |
| turn | Yes | fraction of residues favouring a turn | |
| atoms | Yes | total number of atoms in the molecule, or null when a residue has no formula | |
| boman | Yes | Boman potential protein-interaction index [kcal/mol] (>2.48 = protein-binding) | |
| gravy | Yes | grand average of hydropathicity over `gravyScale`, or null when a residue has no value on it | |
| helix | Yes | fraction of residues favouring an alpha-helix | |
| sheet | Yes | fraction of residues favouring a beta-sheet | |
| charge | Yes | net charge at `pH` | |
| length | Yes | residues analysed, including any the mass tables have no row for | |
| stable | Yes | ProtParam's own reading of the index: at or below 40. Null exactly when `instability` is — there is no verdict without a value | |
| formula | Yes | molecular formula, ProtParam style (e.g. C1755H2634N466O557S5); empty when a residue has no formula | |
| elements | Yes | atom counts per element (C, H, N, O, S) behind the formula, or null when a residue has no formula | |
| aliphatic | Yes | aliphatic index (Ikai 1980) — higher suggests greater thermostability | |
| nTerminal | Yes | the N-terminal residue the N-end rule half-lives below are read from | |
| gravyScale | Yes | which hydropathy scale `gravy` was averaged over | |
| aromaticity | Yes | aromaticity (Lobry 1994): the F+W+Y frequency, as a fraction | |
| composition | Yes | residue counts, one entry per standard amino acid (ProtParam's composition table) | |
| instability | Yes | instability index (>40 = unstable in vivo), or null when a residue the Guruprasad table has no row for makes it undefined — refused rather than computed on a spliced sequence | |
| momentHelix | Yes | max Eisenberg hydrophobic moment at the α-helix periodicity (100°) | |
| momentSheet | Yes | max Eisenberg hydrophobic moment at the β-sheet periodicity (160°) | |
| nonStandard | Yes | residues with no mass at all (X, B, Z, gaps, *), with their positions: excluded from `mw`, `monoisotopicMw`, `formula` and `elements`, still counted in `length`. Empty on a clean chain | |
| momentWindow | Yes | the window the two moments were measured over, after the clamp to the sequence length — a short peptide is not measured over 11 residues it does not have | |
| halfLifeEcoli | Yes | estimated in-vivo half-life, E. coli (N-end rule) | |
| halfLifeYeast | Yes | estimated in-vivo half-life, yeast (N-end rule) | |
| monoisotopicMw | Yes | monoisotopic molecular weight [Da] — what mass spectrometry reports. Null when a residue has no mass, rather than a mass for a different molecule | |
| scaleNonStandard | Yes | residues that ARE weighed but have no per-residue scale value (U, O). They are why `gravy` and `instability` can come back null on a sequence whose mass is exact | |
| extinctionReduced | Yes | molar extinction coefficient at 280 nm [M-1 cm-1], all cysteines reduced | |
| halfLifeMammalian | Yes | estimated in-vivo half-life, mammalian reticulocytes (N-end rule); '—' when the N-terminus has no entry | |
| compositionPercent | Yes | the same table as mole percent of the chain | |
| extinctionCystines | Yes | molar extinction coefficient at 280 nm [M-1 cm-1], cystines formed (per `cystineConvention`) | |
| gravyHydrophobicEnd | Yes | which end of `gravyScale` is the hydrophobic one: 'higher' (Kyte & Doolittle and most others) or 'lower' (a transfer free energy or a hydrophilicity scale). Read `gravy` against this, never against zero alone | |
| gravyZeroIsMeaningful | Yes | whether `gravyScale` takes both signs. False on the eight one-sided tables (Rose, Miyazawa, Argos, …), where the sign of `gravy` is a property of the scale and says nothing about this protein |