LiteFold/DisProt huggingface dataset:
Protein: DP00026 (UniProt P06179)
Region: residues 455	to 494
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This suggests that there are no significant intrinsic structural constraints in the terminal parts to limit the accessibility of the peptide bonds, i.e. these regions have an exceptionally flexible conformation. The readily hydrolysed terminal portions probably do not have any compact tertiary structure and are in extensive contact with the surrounding media. In contrast, the central region of the molecule, which involves the F40 and F27 fragments is quite stable against proteolysis, indicating that it is probably composed of compact structural units.  
It was found that both termini of flagellin are rapidly degraded in the early steps of proteolysis.
Protein: DP00027 (UniProt P26477)
Region: residues 41	to 97
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The interaction between the flagellum specific sigma factor, sigma 28, and its inhibitor, FlgM, was examined using multidimensional heteronuclear NMR. Here we observe that free FlgM is mostly unfolded, but about 50% of the residues become structured when bound to sigma 28. Our analysis suggests that the sigma 28 binding domain of FlgM is contained within the last 57 amino acids of the protein while the first 40 amino acids are unstructured in both the free and bound states.
Protein: DP00027 (UniProt P26477)
Region: residues 41	to 97
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The interaction between the flagellum specific sigma factor, sigma 28, and its inhibitor, FlgM, was examined using multidimensional heteronuclear NMR. Here we observe that free FlgM is mostly unfolded, but about 50% of the residues become structured when bound to sigma 28. Our analysis suggests that the sigma 28 binding domain of FlgM is contained within the last 57 amino acids of the protein while the first 40 amino acids are unstructured in both the free and bound states.
Protein: DP00027 (UniProt P26477)
Region: residues 41	to 97
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The interaction between the flagellum specific sigma factor, sigma 28, and its inhibitor, FlgM, was examined using multidimensional heteronuclear NMR. Here we observe that free FlgM is mostly unfolded, but about 50% of the residues become structured when bound to sigma 28. Our analysis suggests that the sigma 28 binding domain of FlgM is contained within the last 57 amino acids of the protein while the first 40 amino acids are unstructured in both the free and bound states.
The σ28 binding domain of FlgM is in the C-terminal half
Protein: DP00027 (UniProt P26477)
Region: residues 1	to 97
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The interaction between the flagellum specific sigma factor, sigma 28, and its inhibitor, FlgM, was examined using multidimensional heteronuclear NMR. Here we observe that free FlgM is mostly unfolded, but about 50% of the residues become structured when bound to sigma 28. Our analysis suggests that the sigma 28 binding domain of FlgM is contained within the last 57 amino acids of the protein while the first 40 amino acids are unstructured in both the free and bound states. 
The NH-NOE values for 38 of the first 45 N-terminal residues are shown to the left of the ordinate axis. NH-NOEs for the majority of these residues are large and nega-tive ( < -1.0) indicating the region is very flexible.
The flexibility present in the C-terminal half of FlgM is best indicated by periodic breaks in the positive NH-NOE values. Flexibility in this region is also suggested by the smaller than expected positive NH-NOE values.
The NMR resonances for the N-terminal 40 amino acids of FlgM show no significant chemical shift or line shape changes in the presence of cr28. This demonstrates that the N-terminal 40 amino acid residues are disordered whether or not FlgM is bound to cr28.
Protein: DP00028 (UniProt Q13541)
Region: residues 4	to 118
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR  spectra of 4E-BPI displayed  very high  sensitivity due to long relaxation times, typical of unfolded proteins.
Protein: DP00028 (UniProt Q13541)
Region: residues 47	to 66
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although it was reported in an SPR experiment [29] that the interaction between eIF4E and m7GpppA is significantly increased in the presence of 4E-BP1, the present X-ray analysis showed that little structural change of the eIF4E cap-binding pocket is caused by the binding of the 4E-BP1 peptide in the solid state.
Cross-references: PDB:1WKW
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 63
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Using this shorter construct in the presence of the human 4E-BP1 peptide, we obtained diffraction quality crystals and determined the co-crystal structures of Ascaris eIF4E-3 with m 2,2,7 GTP and m 7 GTP ( Table 3 ).
Cross-references: PDB:3M94
PDB:3M93
Protein: DP00028 (UniProt Q13541)
Region: residues 49	to 68
Annotation: translation initiation factor binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A 20 Residue Fragment of 4E-BP1 Binds to eIF4E and Inhibits Translation in Vitro.
Titration of 15N-labeled eIF4E with this peptide produced some, but not all, of the same chemical shift changes as the whole 4E-BP1 (Figure 3C). This indicates that the peptide binds to eIF4E, although it suggests that the peptide does not make as many contacts or bind in quite the same way as the whole 4E-BP1.
Protein: DP00028 (UniProt Q13541)
Region: residues 5	to 118
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of 4E-BP1 is typical of an unfolded protein, although a very shallow minimum at 220-230 nm suggests a minimal amount of helical secondary structure (Figure 2B).
Protein: DP00028 (UniProt Q13541)
Region: residues 1	to 118
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
BP1 protein has a distinctive far-UV CD spectrum typical for a protein in the pre-molten globule state (Fig. 1, curve 2) with a characteristic deep minimum in the vicinity of 200 nm and relatively low ellipticity around 220 nm.
Protein: DP00028 (UniProt Q13541)
Region: residues 49	to 83
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 4E-BP1 and GYF1/2 canonical motifs adopt a helical conformation on the dorsal surface of 4EHP, whereas the noncanonical sequences bind to the lateral surface of 4EHP using a binding mode similar to that described for 4E-BP1 in complex with eIF4E (Fig. 2C–J; Supplemental Fig. S4E,F; Peter et al. 2015a; Sekiyama et al. 2015). 
Cross-references: PDB:5NVN
Protein: DP00028 (UniProt Q13541)
Region: residues 50	to 63
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Seemingly, binding of the 4EBP1 peptide does not appear to affect the cap binding pocket of eIF4E.
Cross-references: PDB:3U7X
Protein: DP00028 (UniProt Q13541)
Region: residues 5	to 118
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We concluded that the purified 4E-BPs have little or no folded structure in solution.
Protein: DP00028 (UniProt Q13541)
Region: residues 4	to 118
Annotation: translation initiation factor binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Furthermore, small but clear changes were observed in the spectra of both 4E-BPs upon addition of an approximately equimolar amount of eIF4E (Figure 4). We concluded that most or all of the unfolded 4E-BP in our samples binds to eIF4E. The broader lines observed for eIF4E upon addition of 4E-BP1 are consistent with the formation of a complex.
Protein: DP00028 (UniProt Q13541)
Region: residues 49	to 83
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structures of Dm eIF4E and Hs eIF4E are similar to the structures of free or bound eIF4E from diverse organisms, and no major conformational changes in the proteins occur upon 4E-BP binding (Figures 1B–1H and S2A) (Gross et al., 2003, Kinkelin et al., 2012, Mizuno et al., 2008, Paku et al., 2012, Papadopoulos et al., 2014, Siddiqui et al., 2012, Umenaga et al., 2011, Volpon et al., 2006).
Cross-references: PDB:4UED
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 64
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
eIF4E was co-crystallised with either an eIF4G- or a 4E-BP-derived peptide (designated 4G and 4EBP, respectively) and one of three of the m7GMP-derived analogues (squaramides 4a and 4f, sulfonamide 7a).
Cross-references: PDB:5EKV
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 67
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both oligopeptides (eIF4GII orange, 4E-BP1 yellow) adopt an L-shaped extended chain/α-helical structure, which interacts with the convex dorsal surface of eIF4E (shown in blue).
Cross-references: PDB:1EJH
PDB:1EJ4
Protein: DP00028 (UniProt Q13541)
Region: residues 50	to 84
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structure of eIF4E Bound to m7GTP and 4E-BP1.
Cross-references: PDB:5BXV
Protein: DP00028 (UniProt Q13541)
Region: residues 50	to 63
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 4E-BP1 peptide binds to the opposite surface of the protein and forms interactions with schistosome eIF4E almost identical to those previously observed in the human eIF4E·4E-BP complex structure (56).
Cross-references: PDB:3HXG
PDB:3HXI
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 66
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The peptide is bound as an α-helix almost perpendicular to the α-helices on the convex side of the β-sheet.
Cross-references: PDB:2JGC
PDB:2JGB
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 64
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystals were obtained for eIF4E complexed with m7GTP and a 4E-BP1 peptide (RIIYDRKFLMECRN).
Cross-references: PDB:2V8X
PDB:2V8W
PDB:2V8Y
Protein: DP00028 (UniProt Q13541)
Region: residues 109	to 118
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We determined the crystal structures of Arabidopsis thaliana Raptor (atRaptor) bound to TOS motif peptides from human 4EBP1...
Protein: DP00028 (UniProt Q13541)
Region: residues 109	to 118
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The key phenylalanine side chain of the TOS consensus21,22 FXΦDΦ (Φ hydrophobic, X any residue) binds to a pocket together with the preceding TOS residue (thereafter F−1 position). In 4EBP1, this unit consists of the Phe114 aromatic ring making π–π stacking interactions with the Gln113 side chain, whereas in S6K1 and PRAS40 the Phe5 and Phe129 aromatic rings make functionally analogous van der Waals contacts with Val4 and Leu128, respectively (Figs 2b to d). 
Cross-references: PDB:5WBJ
Protein: DP00028 (UniProt Q13541)
Region: residues 4	to 118
Annotation: negative regulation of translation (Biological process)
Evidence: translation assay evidence used in manual assertion
Supporting statements:
In reticulocyte lysate assays, our samples of 4E-BP1 and 4E-BP2 inhibited translation in a dose-dependent manner and this was overcome by addition of purified eIF4E (all the experiments described in this paper used mouse eIF4E, which is 99.5% identical to the human protein).
Protein: DP00028 (UniProt Q13541)
Region: residues 49	to 68
Annotation: negative regulation of translation (Biological process)
Evidence: in vitro translation assay evidence used in manual assertion
Supporting statements:
Furthermore, in reticulocyte lysate assays, the peptide inhibited translation in a dose-dependent manner (Figure 5). 
Thus, residues 49−68 of 4E-BP1 are sufficient for eIF4E binding and translation inhibition.
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 64
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows this region becomes ordered when in complex to the translation initiation factor eIF4E and N7-cap derivatives.
Cross-references: PDB:2V8W
PDB:2V8Y
PDB:2V8X
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 67
Annotation: translation initiation factor binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
As discussed above, the ITC data demonstrate that the 4E-BP1 peptide binds to h4EHP. This peptide consists of residues Arg51BP1 to Val67BP1 of human 4E-BP1 and includes the recognition motif that has been defined for eIF4E (Tyr-X-X-X-X-Leu-ϕ (where X is variable and ϕ is Leu, Met or Phe)22., 23.).
Protein: DP00028 (UniProt Q13541)
Region: residues 51	to 67
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The peptide is bound as an α-helix almost perpendicular to the α-helices on the convex side of the β-sheet.
In the structure, the peptide is clearly defined in the electron density for all residues apart from the last.
Cross-references: PDB:2JGB
PDB:2JGC
Protein: DP00028 (UniProt Q13541)
Region: residues 50	to 83
Annotation: eukaryotic initiation factor 4E binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Unlike other class I eIF4Es, neither mouse nor human eIF4E1B interacted with eIF4G, although they bound to eIF4EBP1 and eIF4ENIF1 (Fig. 2D and Appendix Fig. S2F).
Protein: DP00029 (UniProt Q07731)
Region: residues 78	to 113
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:1AGQ
Protein: DP00030 (UniProt P04150)
Region: residues 77	to 262
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We further carried out partial proteolytic digestion experiments with three different proteases (trypsin, chymotrypsin, and Endo Gluc-C) to determine tertiary structural changes in AF1 with or without p38 MAPK-mediated phosphorylation. The results of one such partial proteolysis experiment are shown in Fig. ​3. 
Authors show in Fig. 3 that the peptide is susceptible to all the proteases digestion, indicating the lack of structure in this region.
Protein: DP00030 (UniProt P04150)
Region: residues 77	to 262
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
 As expected, unphosphorylated AF1 shows characteristics of an ID protein, whereas phosphorylated AF1 adopts significantly higher secondary structural elements in it with helical content increased by >50% at the expense of random coil compared to unphosphorylated AF1 (Fig. 2A and Table ​1).
Protein: DP00030 (UniProt P04150)
Region: residues 181	to 244
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
A large number of transcriptional activation domains (TADs) are intrinsically unstructured, meaning they are devoid of a three-dimensional structure. The fact that these TADs are transcriptionally active without forming a 3-D structure raises the question of what features in these domains enable them to function. One of two TADs in human glucocorticoid receptor (hGR) is located at its N-terminus and is responsible for ∼70% of the transcriptional activity of hGR. This 58-residue intrinsically-disordered TAD, named tau1c in an earlier study, was shown to form three helices under trifluoroethanol, which might be important for its activity.
hGR tau1c was one of the IDPs that was studied in the early days before the PreSMo concept was introduced. Since many transcription factors and TADs contain PreSMos, we wanted to learn whether tau1c also contains PreSMos.
Fig. 1 shows a fingerprint region of an 15N-1H heteronuclear single quantum coherence (HSQC) spectrum of hGR tau1c with resonance assignment. Based on the narrow chemical-shift dispersion in both 15N and 1H dimensions, we can confirm its overall unfolded/disordered nature in agreement with the bioinformatics prediction.
Protein: DP00030 (UniProt P04150)
Region: residues 209	to 213
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
Using GR S211-phospho site-specific antibody (Fig. ​1B) and MALDI-TOF MS (Fig. ​1C), we confirmed p38 MAPK-mediated in vitro phosphorylation of AF1.
Protein: DP00030 (UniProt P04150)
Region: residues 77	to 262
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Consistent with previous reports (11, 20, 21), in the case of unphosphorylated AF1, we detected a very weak interaction with each of these coregulatory proteins. These interactions were increased significantly when AF1 was phosphorylated, suggesting that phosphorylation of AF1 facilitates its interaction with all of the three coregulatory proteins tested (Fig. ​5, compare lanes 2 and 3).
Protein: DP00030 (UniProt P04150)
Region: residues 77	to 262
Annotation: TBP-class protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Consistent with previous reports (11, 20, 21), in the case of unphosphorylated AF1, we detected a very weak interaction with each of these coregulatory proteins. These interactions were increased significantly when AF1 was phosphorylated, suggesting that phosphorylation of AF1 facilitates its interaction with all of the three coregulatory proteins tested (Fig. ​5, compare lanes 2 and 3)
Protein: DP00030 (UniProt P04150)
Region: residues 1	to 518
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
a, GR (ribbon model) is partially unfolded, with the N-terminal residues simultaneously gripped by Hsp70CSBD-β and HopDP2, and is threaded through the semi-closed lumen of Hsp90.
The Cryo-EM structure of the of Hsp90-Hsp70-Hop-GR complex, shows this region lacks electron density, indicating it is disordered. 
Cross-references: PDB:7KW7
EMDB:23050
Protein: DP00030 (UniProt P04150)
Region: residues 1	to 500
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Further, we tested the FRET efficiency of GR500 interaction with each of the coregulators in a cotransfection assay. Our results show that GR500 interacts directly with TBP (Fig. ​6B), CBP (Fig. ​5C), and SRC-1 (Fig. ​6D) in the nuclei of GR-deficient CV-1 cells cotransfected with GR500 with or without each coregulator (compare lanes 2 and 3).
Protein: DP00030 (UniProt P04150)
Region: residues 1	to 500
Annotation: TBP-class protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Further, we tested the FRET efficiency of GR500 interaction with each of the coregulators in a cotransfection assay. Our results show that GR500 interacts directly with TBP (Fig. ​6B), CBP (Fig. ​5C), and SRC-1 (Fig. ​6D) in the nuclei of GR-deficient CV-1 cells cotransfected with GR500 with or without each coregulator (compare lanes 2 and 3).
Protein: DP00030 (UniProt P04150)
Region: residues 275	to 279
Annotation: molecular recognition display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Immunoprecipitation of recipient COS-1 cell extracts revealed that K277R and K293R are poorly sumoylated in comparison with wild-type GR (Figures 1A and 1B, lanes 7–8 and 9–10).
Protein: DP00030 (UniProt P04150)
Region: residues 291	to 295
Annotation: molecular recognition display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Immunoprecipitation of recipient COS-1 cell extracts revealed that K277R and K293R are poorly sumoylated in comparison with wild-type GR (Figures 1A and 1B, lanes 7–8 and 9–10).
Protein: DP00031 (UniProt P13255)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The model of amino acid residues 18−44 was built in (2Fo − Fc) maps. (Fo − Fc) maps did not give any significant electron density for amino acid residues 1−17, indicating that these residues were heavily disordered.
Authors are not considering the first Met residue, therefore the disordered region they are referring to is 1-18.
Cross-references: PDB:1NBI
Protein: DP00031 (UniProt P13255)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure was refined by the standard refinement procedure in the X-PLOR protocol. A (2Fo−Fc) map computed after a refinement showed no significant electron density for the amino acid residues 1 to 40, indicating that these residues were heavily disordered.
Authors are not considering the first Met residue, therefore the disordered region they are referring to is 1-41.
Cross-references: PDB:1D2H