LiteFold/DisProt huggingface dataset:
Protein: DP03722 (UniProt P01089)
Region: residues 68	to 92
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Between helix Ib and helix II, there is a long unstructured loop encompassing the residues corresponding to the linker.
Cross-references: PDB:1PSY
Protein: DP03723 (UniProt P23110)
Region: residues 39	to 48
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The average rmsd from the mean for backbone atoms of the most structured regions are 0.52 and 1.01 Å for all heavy atoms, excluding unstructured regions at the N- and C-termini (residues 1−10 and 102 and 103, respectively) and the region between residues 31 and 45.
Cross-references: PDB:1S6D
Protein: DP03723 (UniProt P23110)
Region: residues 68	to 87
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
A long, unstructured loop region (L2) is present between helices Ib and II, encompassing residues Lys30−Gln49. 
Cross-references: PDB:1S6D
Protein: DP03724 (UniProt A0A396GSL0)
Region: residues 33	to 55
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
NCR044 contains one short (A23 to R25, G28 to C30) antiparallel β-sheet and a “whiff” (S11 to E14) of an α-helix. The rest of the peptide was largely disordered and dynamic, even with the tethering afforded by the two disulfide bonds. 
The short helix found between residues 48-52 is too short to be considered as ordered.
Cross-references: PDB:6U6G
Protein: DP03726 (UniProt P40939)
Region: residues 637	to 647
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Residues 261–265 and 637–647 in TFPα and residues 187–192 in TFPβ were not built, due to the lack of densities in these regions.
Cross-references: PDB:5ZQZ
PDB:5ZRV
Protein: DP03727 (UniProt A7KHA7)
Region: residues 24	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The chemical shift differences between NCR169-ox1 and -ox2 revealed structural differences derived from different disulfide linkage patterns (Supplementary Fig. S6B). As shown in Fig. 2B,C a major difference between the two structures was found in the position of the unstructured N-terminal region.
Cross-references: PDB:7CKD
PDB:7CKE
Protein: DP03727 (UniProt A7KHA7)
Region: residues 39	to 50
Annotation: defense response to bacterium (Biological process)
Evidence: zone of inhibition evidence used in manual assertion
Supporting statements:
NCR169M and NCR169CL-ox had stronger activity than NCR169CS-ox. This result suggested that the region corresponding to NCR169M containing lysine residues contributes the most to the antimicrobial activity, as predicted.
NCR169M showed the highest antimicrobial activity against the symbiotic partner, S. meliloti.
Thus, the disordered conformation of the central Lys-rich region of NCR169 is a unique property that is key to membrane binding and antimicrobial activity.
Protein: DP03727 (UniProt A7KHA7)
Region: residues 24	to 39
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
Furthermore, CD spectra suggested that NCR169N-ox and NCR169M have random structures, whereas NCR169CS-ox and NCR169CL-ox contain β-sheets (Supplementary Fig. S10B and S11A).
Protein: DP03727 (UniProt A7KHA7)
Region: residues 39	to 50
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
Furthermore, CD spectra suggested that NCR169N-ox and NCR169M have random structures, whereas NCR169CS-ox and NCR169CL-ox contain β-sheets (Supplementary Fig. S10B and S11A).
Protein: DP03727 (UniProt A7KHA7)
Region: residues 39	to 50
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As expected, NCR169M, NCR169CS-ox, and NCR169CL-ox bound to DMPG liposomes, but NCR169N-ox did not (Supplementary Figs. S11B and S12). This result suggested that the region corresponding to NCR169M, at least residues 24 to 27, is involved in binding to DMPG.
Thus, the disordered conformation of the central Lys-rich region of NCR169 is a unique property that is key to membrane binding and antimicrobial activity.
Protein: DP03728 (UniProt Q6CSX2)
Region: residues 562	to 831
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
To gain insights into the dynamic properties of Atg1EAT in solution, we performed continuous-labeling HDX-MS (29–31). We initially measured deuteron incorporation into isolated Atg1EAT to analyze the overall kinetics of the HDX reaction. Atg1EAT exchanged about 60% of its exchangeable amide hydrogens within 10 s in D2O (Fig. 2 and Figs. S2–S4). The overall exchange characteristics indicate the presence of a large fraction of highly dynamic, solvent-accessible structure.
Protein: DP03728 (UniProt Q6CSX2)
Region: residues 562	to 831
Annotation: Atg1/ULK1 kinase complex (Cellular component)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
On the basis of the SEC-MALS, a molecular mass of 234 kDa was independently obtained (Fig. S6B and Table S1), consistent with a predominant population of Atg1EAT–Atg13350–525–Atg17–Atg31–Atg29 dimers. Taken together with the ITC and HDX-MS data, these results led us to a model for the pathway of Atg1 complex assembly (Fig. 5).
Protein: DP03729 (UniProt Q8IYT8)
Region: residues 168	to 177
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of electron density indicates this region is disordered.
Cross-references: PDB:6QAT
Protein: DP03730 (UniProt Q13627)
Region: residues 481	to 490
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The authors described "a DYRK1A construct comprising the kinase domain (126–490)", however in the PDB the residues between 480-490 are missing
Cross-references: PDB:6EIV
PDB:6EJ4
PDB:6EIJ
PDB:6EIL
PDB:6EIP
PDB:6EIQ
PDB:6EIR
PDB:6EIS
Protein: DP03730 (UniProt Q13627)
Region: residues 481	to 490
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:5A4L
PDB:5A4E
PDB:5A4Q
PDB:5A4T
PDB:5A54
Protein: DP03731 (UniProt Q9UHK0)
Region: residues 486	to 495
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Not surprisingly, per-residue analysis revealed high T1 and T2 values for the unstructured tails of each partner (i.e., segments 84–85 and 149–155 in ZNHIT3 and segment 486–495 in NUFIP1) but also a significant increase in the α3-α4 loop of ZNHIT3.
Cross-references: PDB:5L85
Protein: DP03732 (UniProt Q8NER1)
Region: residues 2	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with a predicted low overall secondary structure content, the [1H, 15N]-TROSY-HSQC-spectra of human TRPV1-IDR, hsTRPV2 and TRPV3-IDR show limited signal dispersion in the 1HN dimension (Fig. 2 A-C), indicating a similar chemical environment of all 1HN nuclei and an inherent lack of stable structural elements.
Cross-references: BMRB:51353
Protein: DP03733 (UniProt Q9Y5S1)
Region: residues 2	to 73
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with a predicted low overall secondary structure content, the [1H, 15N]-TROSY-HSQC-spectra of human TRPV1-IDR, hsTRPV2 and TRPV3-IDR show limited signal dispersion in the 1HN dimension (Fig. 2 A-C), indicating a similar chemical environment of all 1HN nuclei and an inherent lack of stable structural elements.
Cross-references: BMRB:51354
Protein: DP03734 (UniProt Q8NET8)
Region: residues 2	to 119
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with a predicted low overall secondary structure content, the [1H, 15N]-TROSY-HSQC-spectra of human TRPV1-IDR, hsTRPV2 and TRPV3-IDR show limited signal dispersion in the 1HN dimension (Fig. 2 A-C), indicating a similar chemical environment of all 1HN nuclei and an inherent lack of stable structural elements.
Cross-references: BMRB:51355
Protein: DP03735 (UniProt Q9ET78)
Region: residues 331	to 413
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N/1H HSQC spectrum of JP2 DNA binding domain is shown in Fig. 1. Clearly, the cross-peaks in the HSQC spectrum are not well dispersed as typically observed for a well folded protein. Instead, the cross-peaks are clustered in a narrow strip with the backbone amide NH protons resonated in a narrow 1H range from 7.89 to 8.73 ppm, indicating that this JP2 domain is an intrinsically disordered protein (IDP).
Cross-references: BMRB:51405
Protein: DP03737 (UniProt Q8NE35-2)
Region: residues 1	to 426
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far UV CD spectra of the hCPEB3 IDR also shows the hallmarks of a disordered protein, namely a minimum near 200 nm [27]. No spectral features indicative of α-helix and β-sheet; namely, minima at 208, 218, or 222 nm and no maximum at 195 nm, are evident.
Protein: DP03737 (UniProt Q8NE35-2)
Region: residues 1	to 426
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Its fluorescence emission spectra, recorded at temperatures ranging from 2 to 70 °C, show emission maximum > 350 nm. This is consistent with its six Trp residues being solvent exposed and not buried in the hydrophobic core of a folded domain.
Protein: DP03737 (UniProt Q8NE35-2)
Region: residues 1	to 426
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1D 1H and 2D 1H-1H NOESY spectra show 1H signals clustered into narrow bands near the values observed for short, unstructured peptides.
2D 1H-1H NOESY spectrum of the hCPEB3 IDR recorded at 25 ºC showing the 1HN crosspeak region.  The small chemical shift dispersion in 1HN (8.6 to 7.9 ppm) is a typical feature of disordered and unfolded proteins [27].
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 1	to 227
Annotation: pre-molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectroscopy reveals that the protein comprises an extended central helical domain flanked by disordered termini.
By using high-field NMR spectroscopy, we reveal that the protein comprises an extended central helical domain, with apparent coiled-coil propensity, flanked by long, highly disordered N- and C-terminal domains.
The 15N-1H HSQC spectrum of CAHS-8 (Figure 1 A) is typical of an intrinsically disordered protein, with low dispersion in the 1HN dimension.
A) The 15N-1H correlation spectrum is characteristic of an intrinsically disordered protein. B, C) Secondary 13Ca and 13C’ chemical shifts showing strong a-helical propensities from 95– 195, divided into two distinct helices, a1 (E95-F150) and a2 (V167- L194). 15N relaxation (D; 850 MHz, E; 600 MHz), 15N-1H RDCs (F), and PREs (see Figure S1) suggest the protein acts as a disordered chain comprising two highly populated a-helices (303 K) and no persistent tertiary structure.
The tertiary folding of CAHS-8 was probed using paramagnetic relaxation enhancements, with TEMPO-maleimide labelling of positions A134C and A185C. The absence of significant enhancements beyond immediate neighbours indicates an absence of persistent long-range structure (see Figure S1).
The presence of two helices connected by a more flexible linker is supported by the measurement of 15N-1H residual dipolar couplings (RDCs; see Methods in the Supporting Information). The RDCs show a profile typical of IDPs with helical elements that do not specifically interact with each other, as predicted by simulation and experimentally validated in numerous systems. The RDCs exhibit positive values in the helical regions and lower or negative values in the unstructured parts of the chain (Figure 1 f).
We describe the monomeric behaviour of the protein as partially disordered, with a long two-helical domain flanked by long flexible tails.
Cross-references: BMRB:51115
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 1	to 227
Annotation: pre-molten globule (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS measured at 2 mg mL-1 (blue)
The average radius of gyration Rg,av of an ensemble of fully disordered conformers is 47 +/- 10 A, while an ensemble of conformers containing the helical elements (Rg,av = 59 +/- 11 A; see Figure S2) coincides with the experimental radius of gyration, thereby supporting the nature of the ensemble of unfolded chains comprising significant populations of helices a1 and a2.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 95	to 195
Annotation: supramolecular fiber organization (Biological process)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
CAHS-8 shows a strongly concentration-dependent propensity to oligomerize, as illustrated by SAXS, where scattering curves that are characteristic of fibril formation are observed at higher concentrations (Figure 2 A).
Figure 2. Monomeric CAHS-8 forms higher order oligomers as a function of concentration and temperature. A) SAXS measured at
2 mg mL-1 (blue) and 5 mg mL-1 (red). At the higher concentration, the curve shows characteristics associated with fibril formation.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 95	to 195
Annotation: supramolecular fiber organization (Biological process)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
The 13C chemical shifts show strong temperature dependence, revealing a significantly higher helical content at 278 K for helix a2 (see FigureS3). The 15N relaxation is also temperature dependent (Figure 2 C and see also Figure S4), notably higher than that normally observed in intrinsically disordered proteins containing helical elements[21, 22] (see Figure S2), thus supporting the formation of higher order oligomers at lower temperature.
No signals from helix a1 were detected in the 15N-1H HSQC spectrum of a gel formed from 15N-labelled CAHS-8
These observations are compatible with the involvement of a1 in the formation of fibrils that constitute the gel
On the basis of these observations, we propose that the long helical domains of the partially disordered protein associate through coiled-coil-like interactions under certain environmental conditions (low temperature, high concentration) to form oligomers, then fibrils (Figure 5 C), which eventually form a gel-like matrix. Both charged and hydrophobic amino acids in this region are strongly conserved over CAHS proteins from different species. NMR relaxation data also show strong evidence that this region is central to the intermolecular interaction, with signals in this region disappearing at lower temperatures, where higher order oligomerization is favoured, and relaxation rates increasing more in this region than elsewhere.
We propose that this domain mediates homo-dimerization through a coiled-coil interaction, and have experimentally observed the successive formation of oligomers, fibrils, and eventually gels in response to concentration and temperature change.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 95	to 195
Annotation: supramolecular fiber organization (Biological process)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Dynamic light scattering (DLS) measurements were used to map the phase diagram of CAHS-8 by observing the dependence of the decay in the autocorrelation of scattered intensity as a function of temperature and concentration (Figure 2 B). We observe the formation of an apparent physical hydrogel phase at low temperatures and higher concentration, in qualitative agreement with observations from the NMR and SAXS studies.
Phase diagram derived from DLS. Orange represents the isotropic phase, red represents increased oligomerization associated with slight gel formation, and blue represents gel formation.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 95	to 195
Annotation: supramolecular fiber organization (Biological process)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
We used atomic force microscopy (AFM) in liquid and air modes to observe the apparent formation of fibrils that eventually form a dense mesh that resembles a gel and to investigate the nature of these gels. Extension often follows a twisted helix structure comprising paired filaments, exhibiting a pitch of approximately 600 nm (Figure 3 A). AFM was used to follow gel formation, and revealed the generation of fibrillar structures as a function of time (Figure 3 B, see also Figure S3), eventually leading to a dense mesh of fibres (Figure 3 C).
B) Allowing fibrillation to continue whilst the sample is drying shows an increasingly dense matrix of fibrils. C) After the kinetic series from (A) was recorded and the sample fully dehydrated, air imaging displays the entanglement of the fibrils forming a gel. D) Placing a 30 mg mL-1 gel on glass reveals porous structures, comprising cavities with diameters of tens of nanometers.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 1	to 94
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectroscopy reveals that the protein comprises an extended central helical domain flanked by disordered termini.
By using high-field NMR spectroscopy, we reveal that the protein comprises an extended central helical domain, with apparent coiled-coil propensity, flanked by long, highly disordered N- and C-terminal domains.
NMR spectroscopic analysis of the gels formed from 15N-labelled CAHS-8 demonstrates that the intrinsically disordered domains (excluding helix a1) remain flexible in the context of the fibrillar gel (Figure 4 A).
15N spin relaxation rates reveal an overall similar dynamic behaviour of the N- terminal intrinsically disordered region at 303K as the protein in free solution. The 62–72 strand, comprising both hydrophobic and acidic residues, shows elevated R2 values, which suggests increased correlation times, possibly arising from interaction with more rigid elements of the gel.
We describe the monomeric behaviour of the protein as partially disordered, with a long two-helical domain flanked by long flexible tails.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 196	to 227
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectroscopy reveals that the protein comprises an extended central helical domain flanked by disordered termini.
By using high-field NMR spectroscopy, we reveal that the protein comprises an extended central helical domain, with apparent coiled-coil propensity, flanked by long, highly disordered N- and C-terminal domains.
NMR spectroscopic analysis of the gels formed from 15N-labelled CAHS-8 demonstrates that the intrinsically disordered domains (excluding helix a1) remain flexible in the context of the fibrillar gel (Figure 4 A).
The C-terminal domain shows a similar dynamic behaviour to the monomeric phase
We describe the monomeric behaviour of the protein as partially disordered, with a long two-helical domain flanked by long flexible tails.
Protein: DP03738 (UniProt A0A1W0WK50)
Region: residues 95	to 195
Annotation: pre-molten globule to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectroscopy reveals that the protein comprises an extended central helical domain flanked by disordered termini. Upon concentration, the protein is shown to successively form oligomers, long fibres, and finally gels constituted of fibres in a strongly temperature-dependent manner. The helical domain forms the core of the fibrillar structure
By using high-field NMR spectroscopy, we reveal that the protein comprises an extended central helical domain, with apparent coiled-coil propensity
The 13C chemical shifts show strong temperature dependence, reveal- ing a significantly higher helical content at 278 K for helix a2 (see FigureS3). The 15N relaxation is also temperature dependent (Figure 2 C and see also Figure S4), notably higher than that normally observed in intrinsically disordered proteins containing helical elements[21, 22] (see Figure S2), thus supporting the formation of higher order oligomers at lower temperature.
No signals from helix a1 were detected in the 15N-1H HSQC spectrum of a gel formed from 15N-labelled CAHS-8
Signals from helix a2 are visible in the spectrum, but show considerably higher relaxation rates than those in free solution (25 s-1 compared to 10 s-1), which suggests that this domain is tethered to a much larger, or immobile, object.
On the basis of these observations, we propose that the long helical domains of the partially disordered protein associate through coiled-coil-like interactions under certain environmental conditions (low temperature, high concentration) to form oligomers, then fibrils (Figure 5 C), which eventually form a gel-like matrix.
We describe the monomeric behaviour of the protein as partially disordered, with a long two-helical domain flanked by long flexible tails. We propose that this domain mediates homo-dimerization through a coiled-coil interaction, and have experimentally observed the successive formation of oligomers, fibrils, and eventually gels in response to concentration and temperature change.
Protein: DP03739 (UniProt P24588)
Region: residues 300	to 427
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
AKAP5 is an IDP with a well-characterised PxIxIT SLiM that anchors Calcineurin.
The AKAP5c scaffold is highly disordered and monomeric
Two spectroscopic techniques were deployed to assess and delineate regions of nascent structure and to probe the backbone dynamics in AKAP5c: nuclear magnetic resonance (NMR) and circular dichroism (CD). The 15N-HSQC spectrum (Fig. 1b) displays the low 1HN chemical-shift dispersion (0.7 ppm) and narrow line widths typical of disordered proteins.