protein_disorder
Read-only
Intrinsic disorder along a protein by FoldIndex (Prilusky 2005): I_F = 2.785·⟨H⟩ − |⟨R⟩| − 1.151 over a sliding window, where ⟨H⟩ is mean normalized Kyte-Doolittle hydropathy and ⟨R⟩ the mean net charge per residue.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pH | No | pH for the Henderson-Hasselbalch model, ignored by 'net' (default 7.0, the pH the paper's ⟨R⟩ is defined at). Only applies when chargeModel is henderson-hasselbalch. | |
| _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. | |
| pKaSet | No | named pKa set for the Henderson-Hasselbalch model (default IPC_protein, which is idpr's). Values: EMBOSS (EMBOSS (Rice 2000)), DTASelect (DTASelect (Tabb 2002)), Solomons (Solomons (Solomons 1992)), Sillero (Sillero (Sillero 1989)), Rodwell (Rodwell (Rodwell 1982)), Lehninger (Lehninger (Nelson 2017)), Toseland (Toseland (Toseland 2006)), Thurlkill (Thurlkill (Thurlkill 2006)), Nozaki (Nozaki (Nozaki 1971)), Dawson (Dawson (Dawson 1989)), Bjellqvist (Bjellqvist (Bjellqvist 1994)), ProMoST (ProMoST (Halligan 2004)), IPC_protein (IPC_protein (Kozlowski 2016)), IPC_peptide (IPC_peptide (Kozlowski 2016)), Vollhardt (Vollhardt (Vollhardt 2014)). | IPC_protein |
| window | No | sliding window in residues, odd so a window has a centre residue to report at (default 51, the size the FoldIndex paper uses). Short windows expose single loops; long ones report whole domains. | |
| 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. | |
| chargeModel | No | 'net' counts whole charges K+R−D−E, which is what the paper does; 'henderson-hasselbalch' uses fractional charges at `pH`. They answer different questions and only the first is settled by the paper. | net |
| countHistidine | No | count histidine as positive in the 'net' model. False by default: the paper says charged residues at pH 7.0, and His (pKa ~6) is ~9% protonated there, so Uversky's set is K,R vs D,E — exposed because some FoldIndex descendants do count it. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| plot | Yes | the FoldIndex profile as a plot; below zero is predicted disordered | |
| scores | Yes | just the I_F value per window, parallel to `positions` | |
| window | Yes | the window actually used | |
| overall | Yes | whole-protein FoldIndex from the global means — the number the 2005 paper's abstract reports. Below zero = predicted unfolded | |
| windows | Yes | every window: { position, centerResidue, hydropathy, charge, score } — the series a plot draws | |
| boundary | Yes | the Uversky 2000 boundary |⟨R⟩| = 2.785·⟨H⟩ − 1.151 evaluated at this protein's ⟨H⟩ — what `meanNetCharge` is above or below | |
| segments | Yes | runs of consecutive negative windows as 1-based inclusive residue spans, with each run's mean and minimum I_F | |
| unfolded | Yes | whether the whole-protein point sits above that boundary, i.e. predicted natively unfolded | |
| positions | Yes | 1-based centre residue of each window, parallel to `scores` | |
| pKaSetName | Yes | the pKa set actually used, or '' for the 'net' model which needs none | |
| chargeModel | Yes | the charge model actually used | |
| windowCount | Yes | how many windows were scored — the series length, so a fraction can be read back | |
| meanNetCharge | Yes | |⟨R⟩| over the whole chain — the y of the Uversky point | |
| meanHydropathy | Yes | ⟨H⟩ over the whole chain — the x of the Uversky charge-hydropathy point | |
| disorderedWindows | Yes | how many windows score below zero | |
| disorderedFraction | Yes | that count as a fraction of all windows |