LiteFold/DisProt huggingface dataset:
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 66
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
We then acquired CEST data on a sample containing 628 μM 15N-labeled CytRN and 150 μM uridine phosphorylase (udp) half-site double-stranded DNA, which is one of the operator regions specifically recognized by CytRN (33). In the presence of cognate DNA, a distinct third dip in intensity can be clearly discerned in the CEST profile of CytRN D34 at the 15N chemical shift of state B (117.2 ppm) which is the direct result of exchange between free and DNA-bound forms of CytRN (Fig. 4A).
In notable contrast, the exchange broadening incurred by the excited increases by as much as 14 s−1, resulting in substantially larger dispersions in the CPMG profile (Fig. 4F, yellow). CPMG data thus provide a direct validation of the CS-based model, where only the CytRN excited state but not the disordered state binds DNA.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 2	to 65
Annotation: disorder (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
CytR-DBD at low ionic strength conditions and pH 6.0 displays a bimodal behavior, with the major population displaying a peak FRET efficiency at E = 0.47 (implying a relatively expanded structure) and a minor population having a peak FRET efficiency at E = 0.82 (indicating a collapsed structure). This observation clearly demonstrates that the DNA-free CytR-DBD samples a heterogeneous ensemble of conformations in its native ensemble.
The major and minor populations detected in the smFRET efficiency histograms can be assigned to the mostly unfolded state and the compact folded state, respectively.
To further confirm the assignment of the two populations, we examined the effect of denaturant by adding urea (Figure 4A). As the concentration of urea increases, the relative population of the compact form decreases, with a concomitant increase in the expanded state amplitude (Figure 4B). The observation is similar to the standard unfolding transition of two-state proteins and is consistent with the interpretation that the compact and expanded conformations detected in the FRET histograms correspond to the folded-like and unfolded conformations, respectively.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 2	to 65
Annotation: order (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
CytR-DBD at low ionic strength conditions and pH 6.0 displays a bimodal behavior, with the major population displaying a peak FRET efficiency at E = 0.47 (implying a relatively expanded structure) and a minor population having a peak FRET efficiency at E = 0.82 (indicating a collapsed structure). This observation clearly demonstrates that the DNA-free CytR-DBD samples a heterogeneous ensemble of conformations in its native ensemble.
The major and minor populations detected in the smFRET efficiency histograms can be assigned to the mostly unfolded state and the compact folded state, respectively.
To further confirm the assignment of the two populations, we examined the effect of denaturant by adding urea (Figure 4A). As the concentration of urea increases, the relative population of the compact form decreases, with a concomitant increase in the expanded state amplitude (Figure 4B). The observation is similar to the standard unfolding transition of two-state proteins and is consistent with the interpretation that the compact and expanded conformations detected in the FRET histograms correspond to the folded-like and unfolded conformations, respectively.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 2	to 65
Annotation: disorder to order (Structural transition)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Upon increasing the DNA concentration, the relative abundance of the folded fraction increases monotonically. 
The high FRET efficiency population of CytR-DBD increases in the presence of the varied DNA sequences, in agreement with similar results from ensemble binding isotherms.
Thus, these data provide direct and first evidence that even a random DNA sequence having no similarity with the consensus sequence can induce large structural compaction of the protein.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 2	to 65
Annotation: DNA binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Upon increasing the DNA concentration, the relative abundance of the folded fraction increases monotonically. 
The high FRET efficiency population of CytR-DBD increases in the presence of the varied DNA sequences, in agreement with similar results from ensemble binding isotherms.
Thus, these data provide direct and first evidence that even a random DNA sequence having no similarity with the consensus sequence can induce large structural compaction of the protein.
Protein: DP02542 (UniProt P39061)
Region: residues 27	to 265
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Small-angle  X-ray scattering showed DUF959 to be a highly extended, flexible molecule with a maximum dimension of ~23 nm.
The featureless shape of the scattering pattern (Figure 4A), as well as the Kratky plot (Figure 4B) with its lack of any clear maximum, demonstrate the non-globular, flexible and mainly disordered nature of DUF959.
Protein: DP02542 (UniProt P39061)
Region: residues 27	to 265
Annotation: glycosylation display site (Disorder function)
Evidence: deglycosylation assay evidence used in manual assertion
Supporting statements:
Glycosidase treatment demonstrated considerable amounts of O-glycosylation, and expression of DUF959 in HEK293 SimpleCells capable of synthesizing only truncated O-glycans confirmed the presence of N-acetylgalactosamine-type O-glycans. The DUF959 sequence is characterized by numerous Ser and Thr residues, and this accounts for the finding that half of the recombinant protein consists of glycans.
The DUF959 of ColXVIII is rich in mucin-like O-glycosylation.
Protein: DP02542 (UniProt P39061)
Region: residues 27	to 265
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
To characterize the secondary structure content of the DUF959, SRCD spectra were recorded. In this case the spectrum was typical of disordered proteins ,showing a prominent  negative minimum at 198 nm and a relatively low ellipticity near 210 nm  (Figure  3A). No remarkable changes in the secondary structure content  were discovered  when the temperature was increased to 90°C
Protein: DP02542 (UniProt P39061)
Region: residues 27	to 265
Annotation: molecular function regulator (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
As intrinsically disordered regions and their post-translational modifications are often involved in protein interactions, our findings may point towards a role of the flexible mucin-like domain of ColXVIII as an interaction hub affecting cell signaling. Moreover, the MUCL-C18 may also serve as a lubricant at cell-extracellular matrix interfaces.
DUF959 is a mucin-like domain associated with lipid metabolism and glaucoma in humans.
It was recently demonstrated that one of the SNPs in the DUF959 region, rs114139997, p.Gly111Arg, is associated with circulating lipid content and coronary artery disease [92], and that in line with this, genetic polymorphism in the FZ18 region of COL18A1 is associated with fat deposition and obesity [93]. Moreover, lack of the Col18a1 medium and long variants in mice results in markedly reduced adiposity and imbalance in circulating triglycerides [8], and lack of all three variants causes hypertriglyceridemia and increases atherosclerosis [94,95], further supporting the role of ColXVIII in regulating lipid metabolism. As mentioned above, site-specific O-glycosylation by GalNAc-T2 is a critical regulator of lipid metabolism, and DUF959 was found among the GalNAc-T2 targets in liver [85], implicating that O-glycosylation of ColXVIII may regulate its ability to control lipid homeostasis.
Protein: DP02542 (UniProt P39061)
Region: residues 27	to 265
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy indicates a disordered conformation
To characterize the secondary structure content of the DUF959, SRCD spectra were recorded. In this case, the spectrum was typical of disordered proteins, showing a prominent negative minimum at 198 nm and a relatively low ellipticity near 210 nm (Figure 3A). No remarkable changes in the secondary structure content were discovered when the temperature was increased to 90°C (Figure 3B).
In 50% (v/v) TFE, the CD spectrum of DUF959 showed only minor changes towards helical characteristics, and no significant folding was observed (Figure 3C). We did not detect any conformational changes in DUF959 in the presence of dodecyl phosphocholine micelles, which are commonly used to mimic lipid membrane-binding conditions (data not shown).
Protein: DP02543 (UniProt Q9NUM4)
Region: residues 1	to 95
Annotation: molecular adaptor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The N-terminal cytoplasmic domain of TMEM106B has been amazingly implicated in dynamically and transiently interacting with very diverse proteins or complexes, which include endocytic adaptor proteins such as clathrin heavy chain (CLTC) [12]; proteins including CHMP2B of the endosomal sorting complexes required for transport III (ESCRT-III) complex [13); and microtubule-associated protein 6 (Map6) [14].
Protein: DP02543 (UniProt Q9NUM4)
Region: residues 1	to 119
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the structure of the TMEM106B fibril from normal elder shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7X83
EMDB:33054
Protein: DP02543 (UniProt Q9NUM4)
Region: residues 255	to 274
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the structure of the TMEM106B fibril from normal elder shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7X83
EMDB:33054
Protein: DP02544 (UniProt Q04410)
Region: residues 1	to 372
Annotation: molten globule (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The theoretical molecular mass of the recombinant Grh1 is 41,119 Da, but SDS-PAGE analysis (Fig. 2B) resulted in an apparent molecular mass of ca. 45,000 Da. This suggests that the amount of hydrophobic aminoacids that compose Grh1 is smaller than expected for well-structured proteins, a phenomenon similar to what was previously observed for other IDPs
Protein: DP02544 (UniProt Q04410)
Region: residues 1	to 372
Annotation: molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Size exclusion chromatography of the soluble protein on Superdex-200 column, whose result is shown in Fig. 2B, indicates an apparent molecular mass of 45,200 Da. The differences between the expected molecular mass of Grh1 and the values determined from hydrodynamic methods is likely a consequence of the not-fully globular conformation of Grh1 in solution, which has been observed for other proteins rich in disordered regions33, including the GRASP homologue in C. neoformans
Protein: DP02544 (UniProt Q04410)
Region: residues 1	to 372
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of Grh1 in aqueous solution (Fig. 3) has a minimum around 204 nm and a poorly resolved and lower intensity peak at 222 nm, which are features typical of CD spectra of proteins with a high content of unordered structures19. However, the negative peak at 222 nm is an indication of some ordered elements. Although the intensity ratio of the peaks at 222 nm ([−4,264 deg.cm2.dmol−1) and 200 nm (−6,904 deg.cm2.dmol−1) in the CD spectrum of Grh1 is similar to values observed for other proteins in the pre-molten-globule-like state, according to the “double wavelength” plot, [θ]222 vs. [θ]20019, Grh1 does not fit perfectly as a natively unfolded protein based on the estimation of its secondary structure content (11.5% α-helix, 22.1% β-sheet, 17.4% turns, and 49.8% random coil).
The urea-induced unfolding of Grh1 and DGRASP were analyzed by CD and fluorescence spectroscopies. The unfolding monitored by CD spectroscopy (Fig. 4) is a low cooperative transition as seen in the gradual change of the denatured fraction of the protein (fd) calculated from the molar ellipticity at 222 nm. The sigmoid-like transition is not as abrupt as expected for well-structured proteins of similar size19. The low steepness of the transition curve is typical of native molten globules or native coiled proteins and is due to the low percentage of secondary structure
Protein: DP02544 (UniProt Q04410)
Region: residues 1	to 372
Annotation: amyloid fibril formation (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We report here our findings on the amyloidogenic behavior of this GRASP. They are derived from CD, fluorescence using a specific dye, and Congo Red absorbance experiments. The results obtained from this wide range of techniques led us to the conclusion that Grh1 can form amyloid-like structures in conditions that could be reasonably found in the cell. Moreover, we showed that the DGRASP, which is the most conserved region along GRASP family, is sufficient for the fiber formation.
Protein: DP02545 (UniProt P07948)
Region: residues 1	to 62
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The SH4 and UD chemical shifts show the low dispersion typical of disordered regions either alone or when part of the to the USH3 construct.
Protein: DP02545 (UniProt P07948)
Region: residues 1	to 62
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The presence of fuzzy complexes was assessed by chemical shift perturbation, comparing the environment of backbone NH signals from residues in both the SH3 and disordered domains with those of the respective isolated domains. Significant perturbations far from the connecting residues are indicative of interdomain interactions while the retention of low dispersion in the SH4 and UD confirms that these regions remain disordered in the complex.
the initial 18 residues, including the entire SH4 domain, are clearly not affected by the presence of the SH3 domain. Therefore, in the case of Lyn, the fuzzy complex involves only the SH3 and Unique domains.
Protein: DP02545 (UniProt P07948)
Region: residues 1	to 62
Annotation: molecular function regulator (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
the evidence presented here support a general universal mechanism in which the Unique domain of the various SFK acts as a reader of the intracellular environment, by using the exquisite plasticity of the disordered regions, and transmit this information to generate the proper kinase response, through the fuzzy complex with the SH3 domain
We have used nuclear magnetic resonance (NMR) to show the formation of an intramolecular fuzzy complex in LynA and we show that the 21-residue segment (P23 to R43) that is absent in the LynB isoform contains a specific interaction site with the RT-loop of the SH3 domain, thus making the fuzzy complexes formed by the two isoforms, structurally distinct.
Protein: DP02546 (UniProt P16070)
Region: residues 669	to 742
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report the NMR chemical shift assignment of the recombinant intrinsically disordered CD44 cytoplasmic region (669-742)
Shown in Fig. 1 is the 1H–15N HSQC spectrum, exhibiting a relatively narrow proton chemical shift dispersion corresponding well with the expected values for an intrinsically disordered protein. Additional evidence for this is provided in Fig. 2b, showing only relatively small deviations from random coil for most parts of the protein.
Cross-references: BMRB:27625
Protein: DP02546 (UniProt P16070)
Region: residues 153	to 178
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 10 structures were superposed in a folded region, and residues 21-152 were defined, whereas residues 153-178 were poorly defined.
Residues 153-178 are disordered and are not shown.
Cross-references: PDB:2I83
Protein: DP02546 (UniProt P16070)
Region: residues 153	to 170
Annotation: order to disorder (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A and B, ribbon representations of the unbound (A) and HA-bound (B) states of CD44 HABD. All of the α-helices are colored red. The β-strands are colored cyan and green in the Link module region (residues 32-124) and the lobular region (residues 21-31, 125-178), respectively. The C-terminal unfolded regions (residues 170-178 in A and 153-178 in B) are omitted.
Comparisons of the structures and the backbone flexibility of CD44 HABD between its unbound and HA-bound states revealed that the C-terminal region of CD44 HABD became disordered upon HA binding.
This ligand-induced order-to-disorder transition of the C terminus of CD44 HABD provides a plausible explanation for the mechanism underlying the HA-induced CD44-mediated cell migration.
Cross-references: PDB:2I83
Protein: DP02546 (UniProt P16070)
Region: residues 669	to 742
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report the NMR chemical shift assignment of the recombinant intrinsically disordered CD44 cytoplasmic region (669-742)
Shown in Fig. 1 is the 1H–15N HSQC spectrum, exhibiting a relatively narrow proton chemical shift dispersion corresponding well with the expected values for an intrinsically disordered protein. Additional evidence for this is provided in Fig. 2b, showing only relatively small deviations from random coil for most parts of the protein.
Protein: DP02547 (UniProt Q9Y6G9)
Region: residues 388	to 523
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
we first characterized LIC1-C (residues 388–523) by NMR spectroscopy. The 15N-1H heteronuclear single quantum coherence (HSQC) spectrum of LIC1-C at 25°C showed a narrow 7.8 to 8.6 parts per million (ppm) amide-proton chemical shift range, indicating a predominance of structural disorder (Fig 1C). Near-complete backbone resonance assignment was achieved (104 out of the 117 nonproline residues; Fig 1C, S2 Fig). An overlay of 15N-1H HSQC spectra of two smaller constructs, consisting of residues 388–471 and 472–523, reproduced the spectrum obtained from the entire LIC1-C (S2A Fig). This finding indicates that there are no long-range interactions between N- and C-terminal segments of LIC1-C.
the relaxation data show that LIC1-C is intrinsically disordered with large amplitudes of motions faster than nanoseconds. In helix 1 and 2, the amplitudes are smaller and the local reorientation slower but still on the fast timescale. These results support the highly transient character of the helices derived from the SSP score.
Cross-references: BMRB:27401
Protein: DP02547 (UniProt Q9Y6G9)
Region: residues 388	to 523
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Adaptors known to bind LIC1-C include BICD2 and Spindly (SPDL1), which are likely related [15,16], as well as the structurally distinct adaptors HOOK3, RAB11 family-interacting protein 3 (RAB11FIP3; hereafter referred to as FIP3), and RAB-interacting lysosomal protein (RILP) [12,17].
To identify adaptor binding sites in LIC1-C, we recorded 15N-1H HSQC spectra of LIC1-C bound to SPDL1(2–359), BICD2(2–422), and HOOK3(2–239) using molar ratios of 1:0, 1:0.5, and 1:1 (Fig 2A, 2B, 2C and 2D). The spectra obtained from each titration series revealed similar modes of interaction for the three adaptors. Rather than chemical shifts being perturbed, many peaks were significantly attenuated because of binding.
Protein: DP02547 (UniProt Q9Y6G9)
Region: residues 388	to 523
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of LIC1-C corresponded largely to structural disorder. However, there were negative values at 208 nm and a negative shoulder at 222 nm. These features are indicative of residual helical structure, in agreement with our findings from NMR spectroscopy.
Protein: DP02547 (UniProt Q9Y6G9)
Region: residues 388	to 523
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
the light intermediate chain (LIC) subunit of human dynein uses a short helix in its disordered C-terminal region to bind structurally distinct adaptor proteins that connect the motor to specific cargo.
Adaptors known to bind LIC1-C include BICD2 and Spindly (SPDL1), which are likely related [15,16], as well as the structurally distinct adaptors HOOK3, RAB11 family-interacting protein 3 (RAB11FIP3; hereafter referred to as FIP3), and RAB-interacting lysosomal protein (RILP) [12,17].
To identify adaptor binding sites in LIC1-C, we recorded 15N-1H HSQC spectra of LIC1-C bound to SPDL1(2–359), BICD2(2–422), and HOOK3(2–239) using molar ratios of 1:0, 1:0.5, and 1:1 (Fig 2A, 2B, 2C and 2D). The spectra obtained from each titration series revealed similar modes of interaction for the three adaptors. Rather than chemical shifts being perturbed, many peaks were significantly attenuated because of binding.
Protein: DP02547 (UniProt Q9Y6G9)
Region: residues 388	to 523
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
the light intermediate chain (LIC) subunit of human dynein uses a short helix in its disordered C-terminal region to bind structurally distinct adaptor proteins that connect the motor to specific cargo.
Adaptors known to bind LIC1-C include BICD2 and Spindly (SPDL1), which are likely related [15,16], as well as the structurally distinct adaptors HOOK3, RAB11 family-interacting protein 3 (RAB11FIP3; hereafter referred to as FIP3), and RAB-interacting lysosomal protein (RILP) [12,17].
We obtained a KD of 5.7 ± 1.9 μM for the interaction between LIC1(388–523) and SPDL1(2–359) (Fig 2E).