LiteFold/DisProt huggingface dataset:
Protein: DP00345 (UniProt P16535)
Region: residues 884	to 953
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Finally, we tested the conformational behaviors of HlyA and LktA  signal peptides in phospholipid vesicles,  a  lipid bilayer environment which more closely resembles a membrane  compared to the  other  reagents  tested.   Uncharged phospholipids  PC  could not induce an ordered structure (Figure 7G,H), while  the  anionic  phospholipids  (PS,  PG) induced formation of a-helices in both peptides (Figure 7C- F).
Protein: DP00345 (UniProt P16535)
Region: residues 884	to 953
Annotation: localization (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
This confirms that these  short  sequences  contain  information sufficient  for  recognition and transport, and  that no other sequences  are  required.
In order to test the secretion of these signal peptides, C-HA61 or C-LA70 were coexpressed with the transporter proteins HlyB and HlyD in JM83 cells. Cell media were taken at different points during the growth curve. The secreted signal peptides can be detected by Western blot analysis using C494 antibody. As shown in Figure 3 lanes 3, 4, 7, and 8, signal sequence peptides of HlyA and LktA were found in the medium. This secretion requires the presence of both HlyB and HlyD.
Thus, these data show that the signal sequence bearing peptides can be transported by the HlyB/D transporter in a specific manner.
Protein: DP00345 (UniProt P16535)
Region: residues 884	to 953
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Signal peptides were labelled with 15N to facilitate the NMR analysis. A striking feature of the NMR spectra of both is the poor dispersion in the 1H nuclei, possibly indicating the presence of a significant amount of random-coil or unfolded protein conformation [27]. The 15N-nuclei, on the other hand, have reasonable chemical shift dispersion as has been shown previously for this nucleus in unfolded proteins [28,29].
Both peptides contained two regions with NMR parameters that are characteristic of a-helices (Fig. 1). Typical helical NOEs were observed for residues 31-43 and 56-66 of LktA.
Protein: DP00352 (UniProt O33599)
Region: residues 26	to 44
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This implies that 19 residues that are chemically present at the N terminus of our molecule are disordered.
Cross-references: PDB:1QWY
Protein: DP00352 (UniProt O33599)
Region: residues 147	to 182
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-domain (shown at the top of Figure 1) comprises residues 99–316 and can be divided into two ordered regions that are located upstream and downstream of the disordered segment from residue 147 to residue 182.
Cross-references: PDB:1QWY
Protein: DP00352 (UniProt O33599)
Region: residues 108	to 184
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on chemical shift dispersion and bioinformatics, residues downstream 107 are mainly disordered.
Cross-references: BMRB:51662
Protein: DP00352 (UniProt O33599)
Region: residues 108	to 184
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The peaks assigned to the linker region (108–184), on the other hand, are all found within 7.8–8.3 ppm in the 1HN dimension, and the signals overlap considerably.
Cross-references: BMRB:51662
Protein: DP00352 (UniProt O33599)
Region: residues 147	to 182
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-domain (shown at the top of Figure 1) comprises residues 99–316 and can be divided into two ordered regions that are located upstream and downstream of the disordered segment from residue 147 to residue 182.
Cross-references: PDB:1QWY
Protein: DP00353 (UniProt P23202)
Region: residues 1	to 89
Annotation: disorder (Structural state)
Evidence: site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
Using EPR approach, we investigated the structure of isolated Ure2p prion domain in the construct of Ure2p1–89-M, which is tethered on solid support to prevent protein aggregation. We showed that the pattern of site-specific spin label mobility remains unchanged when the buffer is changed from a strong denaturing buffer to a native buffer, suggesting that the structure of Ure2p1–89-M is completely disordered.
Protein: DP00356 (UniProt Q99967)
Region: residues 220	to 270
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The free CITED2 activation domain, residues 220-269, is unstructured in solution as indicated by the absence of secondary structural elements in the circular dichroism spectra (Fig. 2A) and the narrow range of amide proton chemical shifts in the two-dimensional 1H-15N HSQC spectrum of 15N-labeled CITED2 (Fig. 2B).
Protein: DP00356 (UniProt Q99967)
Region: residues 220	to 270
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the complex (Fig. 2A) shows the formation of additional structure compared with the individual proteins, as indicated by a comparison of the spectrum of the complex with the sum of the spectra of the two components.
Protein: DP00356 (UniProt Q99967)
Region: residues 258	to 270
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Measurement of the heteronuclear [1H]-15N NOE for CITED2 in the complex (Fig. 3) shows that the carboxyl-terminal 10 residues are relatively mobile.
The carboxyl-terminal end of CITED2, beyond Asp-257 is disordered and is not shown.
Cross-references: PDB:1R8U
Protein: DP00356 (UniProt Q99967)
Region: residues 222	to 257
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding to TAZ1, there is increased dispersion of the CITED2 amide proton chemical shifts, indicating structure formation (Fig. 2B).
Weak intermolecular NOEs from Asp-258, Phe-259, and Val-260 in the CITED2 flexible tail to the α1 residues Pro-343, Thr-344, and Ala-345 probably reflect transient contacts, because the last 10 carboxyl-terminal residues of CITED2 are apparently unstructured, as indicated by diminished [1H]-15N heteronuclear NOE values (Fig. 3).
Cross-references: PDB:1R8U
Protein: DP00356 (UniProt Q99967)
Region: residues 220	to 270
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The free CITED2 activation domain, residues 220-269, is unstructured in solution as indicated by the absence of secondary structural elements in the circular dichroism spectra (Fig. 2A) and the narrow range of amide proton chemical shifts in the two-dimensional 1H-15N HSQC spectrum of 15N-labeled CITED2 (Fig. 2B).
Protein: DP00356 (UniProt Q99967)
Region: residues 220	to 257
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding to TAZ1, there is increased dispersion of the CITED2 amide proton chemical shifts, indicating structure formation (Fig. 2B).
The changes in chemical shifts for the CITED2 protein upon binding indicate the formation of a helical structure in the N terminus, with an extended structure in the center of the sequence.
Measurement of the heteronuclear [1H]-15N NOE for CITED2 in the complex (Fig. 3) shows that the carboxyl-terminal 10 residues are relatively mobile.
Cross-references: PDB:1R8U
Protein: DP00356 (UniProt Q99967)
Region: residues 220	to 257
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding to TAZ1, there is increased dispersion of the CITED2 amide proton chemical shifts, indicating structure formation (Fig. 2B).
The changes in chemical shifts for the CITED2 protein upon binding indicate the formation of a helical structure in the N terminus, with an extended structure in the center of the sequence.
Measurement of the heteronuclear [1H]-15N NOE for CITED2 in the complex (Fig. 3) shows that the carboxyl-terminal 10 residues are relatively mobile.
Cross-references: PDB:1R8U
Protein: DP00356 (UniProt Q99967)
Region: residues 220	to 257
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The shorter CITED2 construct (residues 220-269) showed high affinity to TAZ1 (Kd = 13 nm, Table I) with less tendency to precipitate upon binding to TAZ1 and was therefore used for structure determination.
Protein: DP00357 (UniProt P62328)
Region: residues 17	to 44
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The assignment of the proton, nitrogen, and carbon resonances of Tβ4 free in solution were obtained using standard procedures. The HSQC spectrum of Tβ4 in solution is typical of an unfolded protein, with a very narrow range of amide proton resonances. NOE correlations for all residues along segment 5-16 indicates that this part of the protein folds as a α-helix.
Protein: DP00357 (UniProt P62328)
Region: residues 17	to 44
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The small negative Hα and positive Cα shifts relative to the random coil shifts observed for residues 31-37 suggest that this segment has a weak tendency to fold into an α-helix. 
The large dispersion of amide proton resonances in the bound form (to CaATP-actin) is typical of a fully structured protein.
Protein: DP00357 (UniProt P62328)
Region: residues 17	to 44
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The large spreading of all resonances of Tβ4 testifies that at 25 °C, Tβ4 forms a tight complex with G-actin, in which the environment of all residues of the peptide is drastically modified, either by folding or by making contacts with G-actin.
Protein: DP00357 (UniProt P62328)
Region: residues 1	to 44
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of free thymosin beta4 is dominated by the deep trough at 200 nm indicating that thymosin beta4 is predominantly in a random coil conformation.  The nonzero value at 222 nm indicates that part of the structure may not be an ideal random coil.
Protein: DP00357 (UniProt P62328)
Region: residues 1	to 44
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of thymosin â4 was also measured in the presence of equimolar actin.
Protein: DP00357 (UniProt P62328)
Region: residues 1	to 44
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The thymosin beta4 spectrum indicated a predominantly random coil structure, but the increased depth of the trough at 222 nm indicated the formation of some additional ordered structure upon binding actin.
Protein: DP00357 (UniProt P62328)
Region: residues 1	to 44
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
One-dimensional 1H NMR spectra of free thymosin beta4 showed narrow line widths and low dispersion, and are consistent with a predominantly random coil structure which is highly mobile on the NMR time scale.
Protein: DP00357 (UniProt P62328)
Region: residues 1	to 44
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The spectrum of thymosin beta4 bound to actin, after subtraction of the actin signal, is very similar to
the spectrum of free thymosin beta4.
Protein: DP00357 (UniProt P62328)
Region: residues 1	to 44
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Overall, the published spectroscopic results and those presented above suggest that in the actin-Tß4 complex, up to 12 residues of thymosin beta4, possibly residues 5-16, are in an alpha-helical conformation, while the rest of the peptide is predominantly in a random coil conformation.
Protein: DP00359 (UniProt A6Q0K5)
Region: residues 1	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
CP12 is an 8.5-kDa nuclear-encoded chloroplast protein, isolated from higher plants. It forms part of a core complex of two dimers of phosphoribulokinase (PRK), two tetramers of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and CP12. Oxidized, but not reduced, CP12 acts as a linker in the assembly of the complex. Reduced CP12 is mainly unstructured
The reduction of oxidized CP12 caused a very large change in the NMR spectrum. All the correlations in the HSQC having chemical shift values different from those of a random coil disappeared, and all the chemical shift values of the correlations were those for a typical unstructured peptide (Figure 5). In addition, all the heteronuclear nOe effects became very negative, indicating that reduced CP12 was much more mobile than the oxidized form. Thus, CP12 became completely unstructured upon reduction, in agreement with the CD experiments.
Protein: DP00359 (UniProt A6Q0K5)
Region: residues 1	to 50
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CP12 is an 8.5-kDa nuclear-encoded chloroplast protein, isolated from higher plants. It forms part of a core complex of two dimers of phosphoribulokinase (PRK), two tetramers of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and CP12. Oxidized, but not reduced, CP12 acts as a linker in the assembly of the complex. Reduced CP12 is mainly unstructured
The reduction of oxidized CP12 caused a very large change in the NMR spectrum. All the correlations in the HSQC having chemical shift values different from those of a random coil disappeared, and all the chemical shift values of the correlations were those for a typical unstructured peptide (Figure 5). In addition, all the heteronuclear nOe effects became very negative, indicating that reduced CP12 was much more mobile than the oxidized form. Thus, CP12 became completely unstructured upon reduction, in agreement with the CD experiments.
Protein: DP00359 (UniProt A6Q0K5)
Region: residues 51	to 60
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Low {1H}–15N het-NOE values (< 0.4), typical of a disordered linker between globular domains, are observed for residues A51–D60
Protein: DP00359 (UniProt A6Q0K5)
Region: residues 51	to 60
Annotation: flexible linker (Disorder function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
the N-terminal region is unstable, oscillates at the ms timescale between helical and random conformations, and is connected through a disordered linker to its C-terminus, which forms a stable helical turn.
Protein: DP00359 (UniProt A6Q0K5)
Region: residues 62	to 78
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In C. reinhardtii, the reduction/oxidation regulation of CP12 is mediated via its four cysteine residues, which are involved into two disulfide bridges under oxidized state (C23–C31 and C66–C75) [28]. The disorder to order transition induced by formation of these disulfide bridges endows CP12 with the same peculiar properties as other IDPs named conditionally disordered proteins.
Protein: DP00359 (UniProt A6Q0K5)
Region: residues 62	to 78
Annotation: disorder to order (Structural transition)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The most drastic differences are in the C-terminal region L62–Y78, indicating that oxidation triggered the folding of this region. The Cα chemical shifts of this region indicate a helical formation.
Protein: DP00377 (UniProt P45577)
Region: residues 130	to 173
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Thus, limited trypsin digestion of purified ProQ yielded protease resistant fragments corresponding to the predicted N- and C-terminal domains. In contrast, fragments corresponding to predicted tryptic fragments within the linker region (amino acids 130−173) were not found.
Protein: DP00377 (UniProt P45577)
Region: residues 130	to 173
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD experiments for the whole protein show a high disordered content that disappear when the N-terminal and C-terminal domains are assessed alone. This indicates that the linker region is disordered.
Protein: DP00377 (UniProt P45577)
Region: residues 130	to 173
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Thus, limited trypsin digestion of purified ProQ yielded protease resistant fragments corresponding to the predicted N- and C-terminal domains. In contrast, fragments corresponding to predicted tryptic fragments within the linker region (amino acids 130−173) were not found.
Protein: DP00380 (UniProt P38582)
Region: residues 59	to 69
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Bacteriocins produced by lactic acid bacteria are potent antimicrobial compounds which are active against closely related bacteria. Producer strains are protected against the effects of their cognate bacteriocins by immunity proteins. However, to date, no structures are available for the corresponding immunity proteins. We report here the NMR solution structure of the 111-amino acid immunity protein for carnobacteriocin B2 (ImB2).
Most of the charged and polar residues in the protein face the solvent. Helix 3 is well-defined to residue 55, and a stretch of nascent helix followed by an unstructured loop joins it to helix 4. The loop between helices 3 and 4, and a hydrophobic pocket which it partially masks, may be important for interaction with membrane receptors responsible for sensitivity to class IIa bacteriocins
Amide cross-peaks were broad and weak for residues 56, 58, 65, 66, 69, and 73 and either overlapped or missing for residues 62, 63, 67, 68, and 74 in 15N HSQC spectra. Some of the side chain 1 H-13C cross-peaks for these residues were also not observed in 13C HSQC spectra. Side chain assignments for residues 55, 59, 62, 67, 68, and 71 were partially determined. Higher temperature (28 °C vs 15 °C) resulted in further broadening of the amide cross-peaks in this region and allowed even fewer assignments to be made. Only intraresidue or i + 1 NOEs were observed for 10 of the 20 amino acid residues in this small section of the protein, which is relatively unstructured and forms a conformationally flexible section (see below).

Because of a lack of NOE data, helix 3 is well defined until only S55 (see below). The nascent helical structure in this region may be forming and dissociating on the NMR time scale, resulting in averaging of chemical shifts and broad peaks that cannot be observed

As mentioned above, helix 3 is well-defined to residue S55, and NOEs indicative of helical structure are observed to residue I58. From residues 58-71, a relatively unstructured loop is apparent. Data indicate a nascent helix structure can be present up to residue 64. This region may be important for binding a putative receptor in the cell membrane (see below).
Cross-references: PDB:1TDP
Protein: DP00381 (UniProt P35869)
Region: residues 545	to 713
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectra are very similar and are dominated by the minimum at around 200 nm, which is indicative of polypeptides with significant nonordered structure.
Protein: DP00381 (UniProt P35869)
Region: residues 545	to 713
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Figure 6 shows that in the absence of TMAO the AhR−AB polypeptide is extremely sensitive to digestion with chymotrypsin with no clear ladder of fragments observed and no full-length polypeptide remaining after 5 min.
Protein: DP00381 (UniProt P35869)
Region: residues 545	to 713
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
 After excitation at 278 nm, the main features observed are a λmax for tryptophan emission at 344 nm (average of 343 ± 2 nm, n = 7) and a shoulder at 307 nm for tyrosine (Figure 4A).
The emission spectra for the soluble and refolded AhR TAD polypeptides were essentially indistinguishable (Figure 4B) (see also below). Taken together, these results suggest that removal of the denaturant, urea, leads to folding of the AhR−AB polypeptide into a relatively open conformation that is intrinsic to the polypeptide and not a consequence of the purification process.
Protein: DP00381 (UniProt P35869)
Region: residues 545	to 713
Annotation: TFIID-class transcription factor complex binding (Molecular function)
Evidence: protein binding evidence used in manual assertion
Supporting statements:
Figure 2 (panels A and B) confirms the interaction with the TBP and also shows interactions with TAF4 and TAF6, other components of the TFIID complex.
Virtually the same levels of TBP binding were observed no matter the method of AhR−AB purification (Figure 2C).
Protein: DP00385 (UniProt P49841)
Region: residues 388	to 392
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
Thus, Thr390 of GSK3β appears to be specifically phosphorylated by p38 MAPK.
Protein: DP00385 (UniProt P49841)
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:
Several sections of the
structure lacked interpretable electron density,
indicating a high degree of disorder. These include
the N-terminal segment 1–34, the loop 120–124
and the C-terminal segment 386–420. In addition,
the electron density was weak for the region 285–
295.
Cross-references: PDB:1Q4L