LiteFold/DisProt huggingface dataset:
Protein: DP01245 (UniProt P12823)
Region: residues 1	to 13
Annotation: flexible N-terminal tail (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The alpha-helical nature of the C protein was confirmed experimentally by far-UV circular dichroism (CD). The far-UV CD spectra of both YFC and DEN2C demonstrated characteristics of alpha-helical proteins with local minima at 222 and 208 and a maximum at 190 nm (data not shown). In addition, the far-UV CD spectra for DEN2CΔ1-13 was essentially identical to that for DEN2C, indicating that removal of the first 13 residues did not significantly perturb the secondary structure of DEN2C (data not shown).
Protein: DP01245 (UniProt P12823)
Region: residues 14	to 23
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The Hα chemical shift changes promoted by the presence of LDs were quantified, showing that the highest changes occurred for the resonances of Asn1, Met2 and Leu3.
To evaluate whether binding of pep14–23 to LDs was also dependent on a surface protein, LD limited proteolysis was performed before zeta potential measurements. As previously observed for C protein, LD trypsinization eliminated the ability of pep14–23 to interact with LDs (Figure 4).
Authors show this fragment binds to an unidentified  protein present in lipid droplets from BHK cells.
Protein: DP01245 (UniProt P12823)
Region: residues 2756	to 2784
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Mass spectrometry analysis of dissolved NS5MTaseDV crystals showed that the C-terminus missing in the structure is present in the crystallized protein. Thus, the C-terminal part appears to be flexible, probably due to the absence of the polymerase domain of NS5.
Cross-references: PDB:1L9K
Protein: DP01245 (UniProt P12823)
Region: residues 1489	to 1660
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As shown in Fig 1A, NS3pro has very similar far-UV CD spectra in Milli-Q water (pH 4.0) and 5 mM phosphate buffer (pH 7.0), with the maximal negative signal at 200 nm and no positive signal below 200 nm, which is typical of a predominantly disordered protein without any stable secondary structure.
The NS3pro 14-185 region corresponds to the 1489-1660 region of the polyprotein.
Taken together, CD and NMR results define the 172-residue NS3pro domain to be an intrinsically disordered protein which is lacking of both stable secondary and tertiary structures in the absence of the NS2B cofactor [22,31–36].
Protein: DP01245 (UniProt P12823)
Region: residues 1489	to 1660
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Moreover, it has a HSQC spectrum with very narrow spectral dispersions at both 1H (~0.9 ppm) and 15N (~19 ppm) dimensions (Fig 1B), further indicating the absence of tight tertiary packing.
Taken together, CD and NMR results define the 172-residue NS3pro domain to be an intrinsically disordered protein which is lacking of both stable secondary and tertiary structures in the absence of the NS2B cofactor [22,31–36].
Protein: DP01245 (UniProt P12823)
Region: residues 1489	to 1660
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The NS3pro domain in complex with NS2B has very large (ΔCα-ΔCβ) deviations characteristic of a well-folded protein.
Taken together, CD and NMR results define the 172-residue NS3pro domain to be an intrinsically disordered protein which is lacking of both stable secondary and tertiary structures in the absence of the NS2B cofactor [22,31–36].
The NS3pro 14-185 region corresponds to the 1489-1660 region of the polyprotein.
Protein: DP01245 (UniProt P12823)
Region: residues 1489	to 1660
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated NS3pro (14–185) and NS2B (48–100) are largely disordered in solution (Fig 3A) and the NS3pro alone showed no detectable catalytic activity even with a protease concentration up to 5 μM in buffers at pH 7.5 (Fig 3B). However, upon mixing them at an equal molar ratio in Milli-Q water at pH 4.0, the mixture has a CD spectrum for a protein with a substantial amount of secondary structures, which has a large positive signal at 190 nm and the maximal negative signal at 208 nm (Fig 3A).
The NS3pro 14-185 region corresponds to the 1489-1660 region of the polyprotein.
Protein: DP01245 (UniProt P12823)
Region: residues 1393	to 1445
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Unfortunately, HSQC peaks of the NS2B (48–100) are much more broadened than those of NS3pro, implying that the isolated NS2B (48–100) has dynamic aggregation or/and conformational exchanges on the μs-ms time scale, thus preventing from further high-resolution NMR studies
The NS2B 48-100 region corresponds to the 1393-1445 region of the polyprotein.
Protein: DP01245 (UniProt P12823)
Region: residues 1393	to 1445
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Interestingly, on the other hand, NS2B (48–100) has a CD spectrum with the maximal negative signal at 206 nm and positive signal at 190 nm, as well as an additional negative signal at 222 nm.
The NS2B 48-100 region corresponds to the 1393-1445 region of the polyprotein.
Protein: DP01245 (UniProt P12823)
Region: residues 1393	to 1445
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated NS3pro (14–185) and NS2B (48–100) are largely disordered in solution (Fig 3A) and the NS3pro alone showed no detectable catalytic activity even with a protease concentration up to 5 μM in buffers at pH 7.5 (Fig 3B). However, upon mixing them at an equal molar ratio in Milli-Q water at pH 4.0, the mixture has a CD spectrum for a protein with a substantial amount of secondary structures, which has a large positive signal at 190 nm and the maximal negative signal at 208 nm (Fig 3A).
The NS2B 48-100 region corresponds to the 1393-1445 region of the polyprotein.
Protein: DP01245 (UniProt P12823)
Region: residues 1393	to 1445
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The NS3pro domain in complex with NS2B has very large (ΔCα-ΔCβ) deviations characteristic of a well-folded protein.
The NS3pro 14-185 region corresponds to the 1489-1660 region of the polyprotein. while the NS2B 48-100 region corresponds to the 1393-1445 region of the polyprotein.
Protein: DP01245 (UniProt P12823)
Region: residues 1489	to 1660
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The NS3pro domain in complex with NS2B has very large (ΔCα-ΔCβ) deviations characteristic of a well-folded protein.
The NS3pro 14-185 region corresponds to the 1489-1660 region of the polyprotein. while the NS2B 48-100 region corresponds to the 1393-1445 region of the polyprotein.
Protein: DP01246 (UniProt O13916)
Region: residues 25	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Full-length Hcn1 was co-crystallized with Cut9; however, only residues 1–24 are clearly visible in the electron density map, and thus the lack of density for residues 25–80 indicates structural disorder.
Protein: DP01248 (UniProt O95292)
Region: residues 1	to 125
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The Pro56Ser mutated version of this peptide, associated with Amyotrophic Lateral Sclerosis (ALS), is intrinsically disordered in solution at pH 3.5–5.5, and aggregates at pH 6.5 due to a loss of stability.
As shown in Figure 4a, at pH 3.5 the Pro56Ser MSP domain has a far-UV CD spectrum characteristic of a predominantly unstructured protein, with its maximal negative signal at ∼199 nm and without any positive signal (30). Interestingly, the overall shapes of the CD curves are very similar at pH 3.5, 4.5, and 5.5, indicating that the mutant remains highly unstructured even at pH 5.5.
Protein: DP01248 (UniProt O95292)
Region: residues 1	to 125
Annotation: order to disorder (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
When the Proline 56 residue is mutated to Serine, variant associated with Amyotrophic Lateral Sclerosis (ALS), the MSP domain loses its native structure and stability, becoming disodered.
As shown in Figure 4a, at pH 3.5 the Pro56Ser MSP domain has a far-UV CD spectrum characteristic of a predominantly unstructured protein, with its maximal negative signal at ∼199 nm and without any positive signal (30). Interestingly, the overall shapes of the CD curves are very similar at pH 3.5, 4.5, and 5.5, indicating that the mutant remains highly unstructured even at pH 5.5.
As shown in Figure 4b, the overall shapes of the CD spectra are still similar at various pH values and salt concentrations up to 10 mM, indicating that the mutant remains similarly disordered under these conditions. However, when the pH value reached 6.5 for the sample containing 10 mM salt, the protein precipitated immediately, and consequently, the CD signal disappeared (Figure 4b).
Protein: DP01248 (UniProt O95292)
Region: residues 125	to 150
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, VAPB(1–150) has a far-UV CD spectrum similar to that of VAPB(1–125) which was previously characterized to adopt a β-dominant MSP fold [46]. This observation implies that the extra C-terminal 25 residues in VAPB(1–150) is largely unstructured and its presence does not alter the MSP-fold.
Protein: DP01248 (UniProt O95292)
Region: residues 125	to 150
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Furthermore, as shown in Figure 1d, most HSQC peaks of VAPB(1–125) are also superimposable to those of VAPB(1–150), indicating that the C-terminal 25 residues of VAPB(1–150) have no significant packing with the MSP fold assumed by the N-terminal 125 residues [46]. Taken together, CD and NMR results demonstrate that VAPB(1–195) is composed two structural domains, namely the well-folded β-dominant MSP fold and helical VAPB-CC linked by the flexible loop.
Protein: DP01248 (UniProt O95292)
Region: residues 1	to 125
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The Pro56Ser mutated version of this peptide, associated with Amyotrophic Lateral Sclerosis (ALS), is intrinsically disordered in solution at pH 3.5–5.5, and aggregates at pH 6.5 due to a loss of stability.
As one can see in Figure 4c, at pH 3.5, the mutant has a HSQC spectrum characteristic of an unfolded protein without any tight tertiary packing, with only 0.8 and 11 ppm dispersions over the 1H and 15N dimensions, respectively (43-46), consistent with the CD results.
It is thus interesting to investigate whether the mutant might have a conformational ensemble similar to that of the unfolded population of the wild type at pH 3.5. However, unlike the wild-type MSP domain which could reversibly fold back at pH >4.5, the Pro56Ser mutant at pH 4.5 and 5.5 still remains highly unstructured as no significant dispersion change is observed for their HSQC spectra (Figure 4d,e). At pH 6.5, the protein completely aggregated, and consequently, no HSQC peaks could be detected (data not shown).
Protein: DP01248 (UniProt O95292)
Region: residues 1	to 125
Annotation: order to disorder (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
When the Proline 56 residue is mutated to Serine, variant associated with Amyotrophic Lateral Sclerosis (ALS), the MSP domain loses its native structure and stability, becoming disodered.
As one can see in Figure 4c, at pH 3.5, the mutant has a HSQC spectrum characteristic of an unfolded protein without any tight tertiary packing, with only 0.8 and 11 ppm dispersions over the 1H and 15N dimensions, respectively (43-46), consistent with the CD results.
It is thus interesting to investigate whether the mutant might have a conformational ensemble similar to that of the unfolded population of the wild type at pH 3.5. However, unlike the wild-type MSP domain which could reversibly fold back at pH >4.5, the Pro56Ser mutant at pH 4.5 and 5.5 still remains highly unstructured as no significant dispersion change is observed for their HSQC spectra (Figure 4d,e). At pH 6.5, the protein completely aggregated, and consequently, no HSQC peaks could be detected (data not shown).
Protein: DP01248 (UniProt O95292)
Region: residues 1	to 125
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As shown in Figure 1b, at pH 6.5, the wild-type MSP domain has a far-UV CD spectrum typical of β-dominant secondary structure, with the maximal negative signal at ∼218 nm and the positive signal at ∼199 nm (32).
Protein: DP01248 (UniProt O95292)
Region: residues 1	to 125
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Consistent with the CD results, at neutral pH the wild-type MSP domain has a HSQC spectrum typical of a well-folded protein (Figure 1c), with 3.2 and 26 ppm spectral dispersions over the 1H and 15N dimensions, respectively.
Protein: DP01249 (UniProt P61073)
Region: residues 1	to 26
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 26 N-terminal residues of CXCR4 did not have interpretable density and are presumed to be disordered
Cross-references: PDB:3OE8
PDB:3ODU
Protein: DP01249 (UniProt P61073)
Region: residues 1	to 24
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 in this region indicates disorder. 
Cross-references: PDB:3OE0
Protein: DP01249 (UniProt P61073)
Region: residues 304	to 319
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 in this region indicates disorder. 
Cross-references: PDB:3OE0
PDB:3OE9
Protein: DP01249 (UniProt P61073)
Region: residues 1	to 27
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 in this region indicates disorder. 
Cross-references: PDB:3OE9
Protein: DP01249 (UniProt P61073)
Region: residues 1	to 34
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 in this region indicates disorder. 
Cross-references: PDB:3OE6
Protein: DP01249 (UniProt P61073)
Region: residues 313	to 325
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 in this region indicates disorder. 
Cross-references: PDB:3OE6
Protein: DP01250 (UniProt P02283)
Region: residues 2	to 27
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unstructured residues are indicated in lower case.
Cross-references: PDB:2PYO
Protein: DP01250 (UniProt P02283)
Region: residues 2	to 34
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift indices obtained from the experimental Cα and Cβ chemical shifts confirm the presence of the histone fold core secondary structure elements with disordered tails for both histones, similar to the human dimer (Fig. 1a).
Cross-references: PDB:7PJ1
Protein: DP01250 (UniProt P02283)
Region: residues 2	to 34
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Chemical shift indices obtained from the experimental Cα and Cβ chemical shifts confirm the presence of the histone fold core secondary structure elements with disordered tails for both histones, similar to the human dimer (Fig. 1a).
Cross-references: PDB:7PJ1
Protein: DP01252 (UniProt P01137)
Region: residues 240	to 261
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In chains G and H, residues 241–258 and 241–249, respectively, are disordered, compared with residues 243–250 in chain A of pro-TGF-β1 alone (Fig. 3A). However, the positions of ordered residues 240 and 251–261 also differ markedly. Thus, residues 240–261 (22 residues) are capable of remodeling to extend away from pro-TGF-β1 and fit into the PC cleavage site.
Protein: DP01252 (UniProt P01137)
Region: residues 257	to 260
Annotation: selective autophagy (Biological process)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
To determine whether the two xLIR of TGF-β mediate LC3 interaction, we generated the W17A/V20A, F257A/L260A, and W17A/V20A/F257A/L260A mutants of TGF-β (Supplementary Fig. 7g). TGF-β interaction with recombinant LC3 (His-LC3) was reduced by W17A/V20A or F257A/L260A, and further decreased by W17A/V20A/F257A/L260A (Supplementary Fig. 7g), suggesting that both xLIR motifs are required for efficient LC3 interaction. In vitro experiments using recombinant GST-pro-TGF-β and His-LC3 confirmed their direct interaction, which was disrupted by W17A/V20A/F257A/L260A (Supplementary Fig. 7h).
The annotated region includes the LIR motif (FLLL) at positions 257-260.
Protein: DP01252 (UniProt P01137)
Region: residues 257	to 260
Annotation: protein binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
To determine whether the two xLIR of TGF-β mediate LC3 interaction, we generated the W17A/V20A, F257A/L260A, and W17A/V20A/F257A/L260A mutants of TGF-β (Supplementary Fig. 7g). TGF-β interaction with recombinant LC3 (His-LC3) was reduced by W17A/V20A or F257A/L260A, and further decreased by W17A/V20A/F257A/L260A (Supplementary Fig. 7g), suggesting that both xLIR motifs are required for efficient LC3 interaction. In vitro experiments using recombinant GST-pro-TGF-β and His-LC3 confirmed their direct interaction, which was disrupted by W17A/V20A/F257A/L260A (Supplementary Fig. 7h).
The annotated region includes the LIR motif (FLLL) at positions 257-260.
Protein: DP01253 (UniProt P05386)
Region: residues 63	to 114
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure of HsP1•HsP2 heterodimer can mainly be divided into two domains–a N-terminal dimerization domain (residue 1–62 of HsP1 and HsP2) and a flexible C-terminal tail, which is composed of the hinge and the highly conserved C-terminal regions (residue 63–114 of HsP1 and 63–115 of HsP2). As a result, the flexible tails of P1•P2 can extend up to ~125 Å away from the N-terminal dimerization domain (Figure 1A).
Protein: DP01253 (UniProt P05386)
Region: residues 63	to 114
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
we propose a model that recruitment of TCS to the sarcin-ricin loop required the flexible C-terminal tail, and the proline-alanine rich hinge region lengthens this C-terminal tail, allowing the tail to sweep around the ribosome to recruit TCS.
Cross-references: PMCID:PMC3794596
Protein: DP01254 (UniProt P12956)
Region: residues 533	to 609
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model is complete with the exception of the disordered Ku70 residues 1–33, 223–230, 533–609 (including the SAP domain), and Ku80 residues 1–5, 171–180, 546–565, plus the disordered final 3 bp of the G-rich stem that occupy a solvent space in the crystal
Protein: DP01255 (UniProt P13010)
Region: residues 546	to 565
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model is complete with the exception of the disordered Ku70 residues 1–33, 223–230, 533–609 (including the SAP domain), and Ku80 residues 1–5, 171–180, 546–565, plus the disordered final 3 bp of the G-rich stem that occupy a solvent space in the crystal
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1450	to 1470
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The C-terminal cytosolic region of NS2B is flexible and disordered as shown by the low NOE values (Figure 2A) of NMR experiments, which corresponds to residues 76-96 of NS2B. Only residues 45-76 are well ordered.
Conversely, residues S48 to D75 of NS2B appear stable in solution, as demonstrated by hetNOE values larger than 0.6 (Fig. 2a).
Cross-references: PDB:5GJ4
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1499	to 1516
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
No electron density is visible for the first 18 amino acids of NS3 protease, indicating that after cleavage the N-terminal region of NS3 protease falls off from its own S′ pocket. Overall, the structure of eZiPro captures the post cleavage state of NS2B-NS3 protease.
Cross-references: PDB:5GJ4
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1499	to 1515
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We then collected the 15N T1, T2, hetNOE parameters and found that residues including S1-E17 and R170 to E177 of the N- and C-termini of NS3pro are highly dynamic in solution, characterized by low T1 and hetNOE values (<0.6) (Fig. 2a).
Cross-references: PDB:5GJ4
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1444	to 1455
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues V76-V87 of NS2B which form a β-hairpin in the crystal structure, are relatively flexible in solution and exhibit relatively broaden peaks, suggesting a dynamic sampling process of the NS2B cofactor binding to NS3 and forming the P2 pocket (Fig. 1b; Supplementary Fig. 6).
Cross-references: PDB:5GJ4