LiteFold/DisProt huggingface dataset:
Protein: DP03407 (UniProt P51397)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The limited spectral dispersion, mainly in the 1HN region, and the lack of defined secondary structure elements, predicted based on chemical shifts, identifies human DAP1 as an intrinsically disordered protein (IDP).
The [1H, 15N]-HSQC spectrum shows a limited signal dispersion in the 1H dimension typically observed for highly flexible or intrinsically disordered proteins. 
The analysis of secondary structure content from the assigned chemical shifts by the CSI web server predicts an all coil formation for the entire human DAP1.
In addition, we analyzed the chemical shift data using the secondary structure propensity (SSP) method to reveal potential structural elements. Even when applying this method no relevant α-helical and β-sheet elements can be detected in the human DAP1 protein. The overall content of α-helical and β-sheet elements estimated by the SSP method amounts to 0% and 14%, respectively. From the experimental data and the structural predictions derived, it becomes clear that the human DAP1 is an intrinsically disordered protein under the chosen conditions.
Cross-references: BMRB:50465
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct studied includes the previously characterized core domain, which incorporates acidic tract A1 (29), and additionally contains the complete N terminus and a disordered C-terminal segment (residues 123–130) containing a CK2 phosphorylation site (Ser125) (20) and acidic tract A2 associated with histone chaperone activity (30).
The N- and C-termini are highly flexible and are not observed in the structure.
Cross-references: PDB:4N8M
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: order to disorder (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra confirmed that, in solution, Npm-N exhibited β-sheet secondary structure in the presence of 0.15 M NaCl (termed the “high-salt” form; Fig. 2C, blue trace). However, in the absence of NaCl (termed the “low-salt” form; Fig. 2C, red trace), Npm-N was disordered.
(C) CD wavelength scans of disordered Npm-N in the absence of NaCl (red) and folded Npm-N in the presence of 0.2 M NaCl (blue).
Npm-N converts from a folded pentamer to a disordered monomer as a function of Na+ concentration.
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: order to disorder (Structural transition)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Velocity sedimentation AUC analysis shows the folded state to be pentameric and the disordered state to be monomeric.
Analysis using sedimentation velocity analytical ultracentrifugation (AUC) confirmed that the high-salt form of Npm-N was pentameric (Fig. 2D, blue trace, and SI Appendix, Table S3) and that the disordered, low-salt form was an elongated monomer (Fig. 2D, red trace, and SI Appendix, Table S3).
Npm-N converts from a folded pentamer to a disordered monomer as a function of Na+ concentration.
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, in the absence of NaCl (termed the “low-salt” form; Fig. 2C, red trace), Npm-N was disordered.
(C) CD wavelength scans of disordered Npm-N in the absence of NaCl (red) and folded Npm-N in the presence of 0.2 M NaCl (blue).
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Analysis using sedimentation velocity analytical ultracentrifugation (AUC) confirmed that the high-salt form of Npm-N was pentameric (Fig. 2D, blue trace, and SI Appendix, Table S3) and that the disordered, low-salt form was an elongated monomer (Fig. 2D, red trace, and SI Appendix, Table S3).
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: order (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Analysis using sedimentation velocity analytical ultracentrifugation (AUC) confirmed that the high-salt form of Npm-N was pentameric (Fig. 2D, blue trace, and SI Appendix, Table S3) and that the disordered, low-salt form was an elongated monomer (Fig. 2D, red trace, and SI Appendix, Table S3).
 (D) Velocity sedimentation AUC analysis shows the folded state to be pentameric and the disordered state to be monomeric.
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra confirmed that, in solution, Npm-N exhibited β-sheet secondary structure in the presence of 0.15 M NaCl (termed the “high-salt” form; Fig. 2C, blue trace).
(C) CD wavelength scans of disordered Npm-N in the absence of NaCl (red) and folded Npm-N in the presence of 0.2 M NaCl (blue).
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These findings were confirmed by using NMR spectroscopy; 2D [1H,15N] TROSY (33) spectra showed that the high-salt form of Npm-N was folded (Fig. 2E, blue spectrum) in a conformation consistent with that observed in the crystal structure (SI Appendix, Fig. S3A), and that the low-salt form was disordered (Fig. 2E, red spectrum, and SI Appendix, Fig. S3B).
(E) Two-dimensional transverse relaxation-optimized spectroscopy (TROSY) spectral overlay of the monomeric (red) and pentameric (blue) folds of 2H/15N-labeled Npm-N.
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: order to disorder (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These findings were confirmed by using NMR spectroscopy; 2D [1H,15N] TROSY (33) spectra showed that the high-salt form of Npm-N was folded (Fig. 2E, blue spectrum) in a conformation consistent with that observed in the crystal structure (SI Appendix, Fig. S3A), and that the low-salt form was disordered (Fig. 2E, red spectrum, and SI Appendix, Fig. S3B).
(E) Two-dimensional transverse relaxation-optimized spectroscopy (TROSY) spectral overlay of the monomeric (red) and pentameric (blue) folds of 2H/15N-labeled Npm-N.
Protein: DP03409 (UniProt Q61937)
Region: residues 1	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These findings were confirmed by using NMR spectroscopy; 2D [1H,15N] TROSY (33) spectra showed that the high-salt form of Npm-N was folded (Fig. 2E, blue spectrum) in a conformation consistent with that observed in the crystal structure (SI Appendix, Fig. S3A), and that the low-salt form was disordered (Fig. 2E, red spectrum, and SI Appendix, Fig. S3B).
(E) Two-dimensional transverse relaxation-optimized spectroscopy (TROSY) spectral overlay of the monomeric (red) and pentameric (blue) folds of 2H/15N-labeled Npm-N.
Protein: DP03409 (UniProt Q61937)
Region: residues 121	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The construct studied includes the previously characterized core domain, which incorporates acidic tract A1 (29), and additionally contains the complete N terminus and a disordered C-terminal segment (residues 123–130) containing a CK2 phosphorylation site (Ser125) (20) and acidic tract A2 associated with histone chaperone activity (30).
The N- and C-termini are highly flexible and are not observed in the structure.
Protein: DP03410 (UniProt Q91MK1)
Region: residues 267	to 336
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Conversely, residues from the flexible linker (amino acids 267–336) are poorly dispersed in the proton dimension, ranging from 8.06 ppm (A318) to 8.61 ppm (S334).
The disordered linker is not, however, a statistical random-coil over its entire length. The temperature-dependent attenuation of 1H–15N HSQC peak intensities is particularly pronounced for residues 279–287. This correlates with observed chemical shift deviations from random coil values, as well as the predicted helical propensity of the sequence (not shown).
Cross-references: BMRB:27634
Protein: DP03410 (UniProt Q91MK1)
Region: residues 267	to 336
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The phosphoprotein is the non-catalytic subunit of the polymerase, and its C-terminal region enables the polymerase to engage with the nucleocapsid. Here, we report the 1H, 15N, and 13C chemical shift assignments of the C-terminal region (amino acids 267-388) of the Menangle virus phosphoprotein. This region has a bipartite character, with a highly flexible and structurally disordered sequence preceding a structured nucleocapsid-binding domain.
Conversely, residues from the flexible linker (amino acids 267–336) are poorly dispersed in the proton dimension, ranging from 8.06 ppm (A318) to 8.61 ppm (S334).
Protein: DP03410 (UniProt Q91MK1)
Region: residues 267	to 328
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
the Kratky plot for the isolated linker (L) increases monotonically with the scattering angle, which is characteristic of unfolded proteins
Although the analytic expression describing the scattering of the worm-like chain (Equation 6) involves approximations which are strictly valid only for long chains (L/b > 10), and at low scattering angles (qb < 3) [53,54], the model fits the data very well over the q range 0.015–0.30 Å−1 (Figure 5). The SAXS analysis therefore confirms that the linker has an extended conformation with no significantly populated tertiary structure.
In Menangle virus, the ~62 residue linker is also globally disordered and lacks any tertiary structure. This is readily apparent from model-free analysis of the SAXS data (Figure 4).
Cross-references: SASBDB:SASDLJ9
Protein: DP03410 (UniProt Q91MK1)
Region: residues 267	to 328
Annotation: flexible linker (Disorder function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We investigate the oligomerization state of the MenV P protein in solution, as well as the structural characteristics of the flexible linker that connects the coiled-coil and the C-terminal binding domain.
The Kratky plot (Figure 4) for the entire C-terminal region (CC-L-BD) has a bell-shaped appearance, consistent with the major scattering contribution coming from the two structured domains (CC and BD) positioned at either end of the chain. In contrast, the Kratky plot for the isolated linker (L) increases monotonically with the scattering angle, which is characteristic of unfolded proteins [76]. The Kratky plot for L-BD has a hybrid appearance, reflecting its nearly equal partition between structured and unstructured regions. 
Cross-references: SASBDB:SASDLJ9
Protein: DP03410 (UniProt Q91MK1)
Region: residues 267	to 328
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As expected, backbone amide resonances associated with the linker (L) showed very limited chemical shift dispersion in the proton dimension, consistent with global disorder, while those associated with the binding domain (BD) were widely dispersed, consistent with overwhelming population of the folded state [61]. The propensity for structure formation in the linker was assessed using the ncSPC algorithm (Figure S4B), based on the weighted deviation of the chemical shifts of five backbone nuclei (1Hα, 13CO, 13Cα, 13Cβ, 15N) from reference values specific for intrinsically disordered proteins [83].
Cross-references: BMRB:27634
Protein: DP03411 (UniProt Q61081)
Region: residues 1	to 144
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We found that a cloud of peaks was present around the center of the spectrum (~ 8 ppm along the 1H axis). Although a small number of exceptional peaks appeared separately from the others, most overlapped with each other as the result of severe line broadening.
These observations suggest that the N-terminal fragment Cdc37(1–144) did not adopt a single rigid conformation under neutral conditions, but that it was in dynamic equilibrium between several different structures, probably between an α-helical and random coil-like structure.
Protein: DP03411 (UniProt Q61081)
Region: residues 1	to 144
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Because the ellipticity value of the CD spectrum is temporally and spatially averaged, its intensity directly depends on the stability or lifetime of α-helical conformations. That is, smaller CD signals could be recorded when the α-helical conformation adopted by each residue was not very stable, but transiently disappeared during measurement of the spectrum. In other words, the secondary and tertiary structures of the protein are not fixed to a single α-helical conformation, but change dynamically between two or more different conformational states.
Protein: DP03411 (UniProt Q61081)
Region: residues 1	to 144
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
This is partly supported by the near-UV CD spectra. Although the spectra indicate that the protein has a certain degree of tertiary structure (well-ordered packing of sidechain of aromatic amino acids) under the neutral conditions, the signal is very weak.
Protein: DP03411 (UniProt Q61081)
Region: residues 11	to 15
Annotation: phosphorylation display site (Disorder function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
These physiological functions are considered to depend on phosphorylation at conserved Ser13 by protein kinase CK2α. To assess whether such chemical modification at the sidechain of aminoacids affects the conformational states of Cdc37, we attempted to prepare phosphorylated Cdc37(1–93) by incubating with CK2α. We first examined whether a phosphorylation reaction occurred in this small N-terminal fragment protein using Phos-tag SDS-PAGE, in which Phos-tag acrylamide gel specifically chelates phosphorylated residues in a protein and retards its migration during electrophoresis. The results clearly demonstrated that the smaller fragment Cdc37(1–93) was indeed phosphorylated by CK2α.
Protein: DP03412 (UniProt P27395)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Prediction of JEVC secondary structure derived on its backbone NMR chemical shifts by TALOS+. The predicted secondary structure elements obtained with TALOS+ are shown as red bars for α-helices.
In Figure 2 the chemical shift-derived secondary structure elements only start at residue 30.
The peaks belonging to residues 1-25 in the HSQC spectrum show a very narrow dispersion.
Cross-references: BMRB:50839
Protein: DP03412 (UniProt P27395)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 25 residues at the N-terminus are not visible in the electron density map.
Cross-references: PDB:5OW2
Protein: DP03413 (UniProt P49880)
Region: residues 564	to 776
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Our results showed that AaFEcR belongs to a family of intrinsically disordered proteins (IDPs) and possesses putative pre-molten globule (PMG) characteristics.
Far-UV circular dichorism (CD) spectroscopy was used to determine the secondary structure content in AaFEcR. Typical for IDPs features were observed for the native spectrum (Fig. 3A), such as: the presence of a minimum at ∼200 nm and the lack of a distinct minima at 208 nm and 222 nm [45]. 
The results obtained for AaFEcR, compared with data for coil-like and PMG-like IDPs, placed AaFEcR among PMG-like IDPs (Fig. 3D).
Protein: DP03413 (UniProt P49880)
Region: residues 564	to 776
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Our results showed that AaFEcR belongs to a family of intrinsically disordered proteins (IDPs) and possesses putative pre-molten globule (PMG) characteristics.
Sedimentation velocity analytical ultracentrifugation (SV-AUC) and a series of size exclusion chromatography (SEC) were conducted in order to determine hydrodynamic properties of AaFEcR. The value of the Stokes radius (RS) for the native AaFEcR is 2.67 nm ± 0.1 nm (Figs. 4A and 5 ). Using equations derived from [46], theoretical values of RS for AaFEcR considered as a native globular protein, a natively unfolded (NU) coil and a NU-PMG were calculated, plotted together with the value obtained experimentally and presented in Fig. 5. The most similar to determined by SEC RS value was the one calculated for NU-PMG, what confirms the results obtained from CD spectroscopy analysis (Fig. 3D).
Protein: DP03413 (UniProt P49880)
Region: residues 564	to 776
Annotation: pre-molten globule (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Our results showed that AaFEcR belongs to a family of intrinsically disordered proteins (IDPs) and possesses putative pre-molten globule (PMG) characteristics.
Sedimentation velocity analytical ultracentrifugation (SV-AUC) and a series of size exclusion chromatography (SEC) were conducted in order to determine hydrodynamic properties of AaFEcR.
The sedimentation coefficient distributions (Fig. 4C) calculated from the SV-AUC data indicate that one major species with a sedimentation coefficient of approximately 1.2 S and a hydrodynamic radius (Rh) slightly greater than 2.9 nm is present in all samples of AaFEcR at different concentrations ranging from 0.15 mg/ml to 1.0 mg/ml range (Table 1).
The frictional ratio (f/f0) of 1.9–2.0, higher than the approximate value of 1.3 expected for a typical globular protein such as bovine serum albumin (BSA), indicates that the protein has an extended conformation. The relation between the frictional ratio and the molecular weight of a protein is an indicative of protein disorder [48].
Fitting the apparent molecular weight (MWapp) of AaFEcR calculated using the SV
data for all three tested concentrations indicated existence of AaFEcR as a monomer.
Protein: DP03413 (UniProt P49880)
Region: residues 564	to 776
Annotation: metal ion binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Using SEC, SV-AUC and ESI-TOF MS, we showed that the intrinsically disordered AaFEcR is able to bind metal ions and form complexes with these ions. 
Injected samples were prepared to determine the specific molar ratio between metal ions and AaFEcR (nM2+/nAaFEcR). For all samples with nM2+/nAaFEcR equal to 0.05, the AaFEcR RS slightly increased. A difference in the ion-AaFEcR interaction was observed for samples with higher metal ion/protein ratios. For the samples of AaFEcR containing Ca2+ (up to a 2.5-fold excess) the overall range of observed changes in the RS values was much smaller than in the presence of Zn2+ or Cu2+.
To investigate in detail whether AaFEcR is capable of binding Zn2+ and Cu2+, we conducted appropriate experiments using CD, SEC and MS techniques. The results clearly showed that recombinant AaFEcR is able to form complexes with Zn2+ and Cu2+, but the interactions result in the protein shrinking rather than structuring.
Protein: DP03413 (UniProt P49880)
Region: residues 564	to 776
Annotation: metal ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Using SEC, SV-AUC and ESI-TOF MS, we showed that the intrinsically disordered AaFEcR is able to bind metal ions and form complexes with these ions. 
The effect of the presence of metal ions on the possible secondary structure formation in AaFEcR was examined with CD spectroscopy. The obtained CD spectra for samples containing AaFEcR with the appropriate metal ion concentration (data not shown) did not indicate significant secondary structure formation. 
To investigate in detail whether AaFEcR is capable of binding Zn2+ and Cu2+, we conducted appropriate experiments using CD, SEC and MS techniques. The results clearly showed that recombinant AaFEcR is able to form complexes with Zn2+ and Cu2+, but the interactions result in the protein shrinking rather than structuring.
Protein: DP03413 (UniProt P49880)
Region: residues 564	to 776
Annotation: metal ion binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Using SEC, SV-AUC and ESI-TOF MS, we showed that the intrinsically disordered AaFEcR is able to bind metal ions and form complexes with these ions.
The mass spectrometric observations are in excellent agreement with the dependencies
observed in Fig. 4D, which shows that the RS of the protein decreased upon the addition of Zn2+ and Cu2+, while no pronounced changes were observed in the presence of Ca2+. MS shows that AaFEcR is able to bind two Zn2+ and Cu2+ ions and only one Ca2+ ion when the metal-to-ligand ratio = 2:1.
To investigate in detail whether AaFEcR is capable of binding Zn2+ and Cu2+, we conducted appropriate experiments using CD, SEC and MS techniques. The results clearly showed that recombinant AaFEcR is able to form complexes with Zn2+ and Cu2+, but the interactions result in the protein shrinking rather than structuring.
Protein: DP03414 (UniProt P40949)
Region: residues 33	to 253
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We used circular dichroism and NMR spectroscopy to show that, unlike the structured TasA, TapA is disordered. In addition, TapA is composed of two weakly interacting domains: a disordered C-terminal domain and a more structured N-terminal domain.
The CD spectrum of a recombinant TapA (expressed in
E. coli, see the Supporting Information for more details)
showed that TapA was partially disordered, according to the
minimum at about 200 nm that was typical for disordered proteins (Figure 1 B).
The secondary structures of the polypeptides were then
determined by means of CD spectroscopy. The CD spectra of
FL TapA and the CTD and NTD fragments (Figure 2 B) show
that, similarly to the FL protein, the CTD and NTD were disordered, but to different extents.
Protein: DP03414 (UniProt P40949)
Region: residues 33	to 253
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The earlier elution of TapA in SEC, relative to a globular protein with the same mass, is expected for disordered proteins due to their extended hydrodynamic radius.
CD analysis, together with the analytical SEC and SEC-MALS results, indicated that TapA was a partially disordered monomer.