LiteFold/DisProt huggingface dataset:
Protein: DP03896 (UniProt Q13635)
Region: residues 1177	to 1447
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The density of residues 1–75 (N-terminal domain), 608–618 and 721–729 (TM6-TM7 linker), 888–901 (in ECD-II) and 1177–1188 (C-terminus) is not resolved nor built.
The PDB shows the protein lacks electron density in this region, indicating it is disordered."
Cross-references: PDB:6OEV
PDB:6OEU
Protein: DP03896 (UniProt Q13635)
Region: residues 614	to 728
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The atomic model of PTCH1Δ-ShhNC24II covers the sequence of PTCH1 residues D46-P1186, with an unresolved loop region comprising residues F614-T728.
Cross-references: PDB:6RMG
EMDB:EMD-4936
Protein: DP03897 (UniProt Q9UII6)
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 final model included residues 25−193 of monomer A and monomer B, residues 25–198 of monomer C and monomer D, and 260 water molecules.
TMDP (25–198) is found to be folded into a compact and globular molecule with approximate dimensions of 40 × 35 × 30 Å3.
Cross-references: PDB:2GWO
Protein: DP03898 (UniProt P80041)
Region: residues 328	to 339
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structures of all three crystal forms of DDC, a short stretch of 11 amino acids (residues 328–339) is invisible in the electron density map. These residues belong to a mobile loop that seems to be important for the catalytic mechanism29,30.
Cross-references: PDB:1JS3
PDB:1JS6
Protein: DP03898 (UniProt P80041)
Region: residues 477	to 486
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 477–486 are completely missing in the structure and are presumably disordered.
Cross-references: PDB:1JS3
PDB:1JS6
Protein: DP03899 (UniProt A0A2V2WGW5)
Region: residues 5	to 23
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Importantly, structures of terminal tails of several essential eIFs in most of the available cryo-EM reconstructions are also lacking, mainly due to their intrinsic flexibility. Among them stand out the terminal tails of the c and d subunits of eIF3, eIF2β, eIF1, and eIF1A, which are all critically involved in scanning and AUG recognition.
The Putative eukaryotic translation initiation factor 1A (eIF1A) takes part in the 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase and the  cryo-EM reconstruction corresponds to the entire complex.
Cross-references: EMDB:11893
PDB:7ASE
Protein: DP03900 (UniProt P16641)
Region: residues 701	to 710
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The flexible loop at 671–680 was rarely observed in electron density maps and was not included in the final models of SmTK chain A, SmTK-Arg chain A, and SmTK-TSA chain B.
Segment 671–680 of the C-terminal region of D2 is not visible in electron density maps (Fig. 1B).
The loop is delineated by two glycine residues (Gly670–Gly681) that account for its high flexibility.
The flexible loop is in red in D1 and shown with a dotted line in D2 because it is not observed in the electronic density maps. 
A Mg2+ ion is only observed in the active site of D1, and the flexible loop is disordered in both lobes.
The disordered conformation of this loop observed in D2 allows equal access to the active site and is consistent with solution NMR measurements performed with AK (68) and CK (30).
The region 671-680 referred to by the authors corresponds to 701-710 residues of the UniProt sequence.
Cross-references: PDB:4WO8
PDB:4WOD
Protein: DP03901 (UniProt A0A504XZ90)
Region: residues 1	to 29
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structure of residues 1-29 is unresolved in the cryo-EM reconstructions, showing its intrinsic flexibility when this protein takes part in the Large subunit from Leishmania major mitochondrial ribosome
Cross-references: PDB:7AM2
EMDB:11821
Protein: DP03901 (UniProt A0A504XZ90)
Region: residues 184	to 237
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structure of residues 184-237 is unresolved in the cryo-EM reconstructions, showing its intrinsic flexibility when this protein takes part in the Large subunit from Leishmania major mitochondrial ribosome
Cross-references: PDB:7AM2
EMDB:11821
Protein: DP03902 (UniProt A0A504WW14)
Region: residues 1	to 1259
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structure of residues 1-1259 is unresolved in the cryo-EM reconstructions, showing its intrinsic flexibility when this protein takes part in the Large subunit from Leishmania major mitochondrial ribosome
Cross-references: PDB:7AM2
EMDB:11821
PDB:7AIH
EMDB:11796
Protein: DP03903 (UniProt Q869A5)
Region: residues 76	to 116
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In both oxidized and reduced Px III, the peroxidatic Cys47 is located on the first loop (L1) between β-strand 1 and α-helix 1, whereas the resolving Cys95 is part of the long loop 2 (L2) between β-sheet 2 and α-helix 2 that is relatively disordered in the bundle of NMR structures (Figs. 2, B and C).
Cross-references: PDB:2RM6
PDB:2RM5
Protein: DP03907 (UniProt Q8TDP1)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:3P56
Protein: DP03907 (UniProt Q8TDP1)
Region: residues 87	to 117
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Therefore, our structural, biochemical and primary sequence analyses are all consistent with RNASEH2C residues 87–117 forming a disordered loop, while RNASEH2C residues 118–160 comprise an integral part of the heterotrimer, essential for complex formation and enzymatic activity.
Cross-references: PDB:3P56
Protein: DP03907 (UniProt Q8TDP1)
Region: residues 93	to 107
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:3PUF
Protein: DP03908 (UniProt P84243)
Region: residues 1	to 38
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The x-ray structures of the RNA polymerase II elongation complex stalled at different SHL show this region of the Histone H3.3 lacks electron density, indicating it is disordered.
Cross-references: PDB:6INQ
PDB:6A5O
PDB:6A5L
PDB:6A5T
PDB:6A5U
PDB:6A5R
PDB:6A5P
Protein: DP03909 (UniProt P36156)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to absence or weakness of electron density in some regions, all monomers built in the structures lacked about thirty residues at similar positions, namely the ten first N-terminal ones (fifteen in monomer B of ScECM4-SG), the 6 histidine residues from the C-terminal tag and residues between D83 and L95.
The lack of electron density upstream G11 suggested a relative flexibility of the first residues.
Cross-references: PDB:5LKB
PDB:5LKD
Protein: DP03909 (UniProt P36156)
Region: residues 84	to 93
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to absence or weakness of electron density in some regions, all monomers built in the structures lacked about thirty residues at similar positions, namely the ten first N-terminal ones (fifteen in monomer B of ScECM4-SG), the 6 histidine residues from the C-terminal tag and residues between D83 and L95.
Residues 84-93 are missing in all chains.
Cross-references: PDB:5LKB
PDB:5LKD
Protein: DP03910 (UniProt Q8WQX9)
Region: residues 576	to 585
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Following crystallization, the TbrPDEB1 structure with residues 586–918 could be resolved by X-ray diffraction at a resolution of 1.65 Å (Table 1).
Cross-references: PDB:4I15
Protein: DP03910 (UniProt Q8WQX9)
Region: residues 565	to 585
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:5G2B
PDB:5G57
PDB:5L8Y
PDB:5L8C
PDB:5L9H
PDB:5G5V
Protein: DP03911 (UniProt Q86C09)
Region: residues 64	to 73
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:2P1C
Protein: DP03912 (UniProt P77526)
Region: residues 205	to 215
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ten residues at the C-terminal are not seen in the electron density map.
The last 11 residues are missing in the structure and are presumably disordered.
Cross-references: PDB:3GX0
Protein: DP03913 (UniProt P0AFW0)
Region: residues 101	to 114
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit contains two molecules of RfaH (see Figure S1 in the Supplemental Data available with this article online); each protomer consists of two domains (N and C terminal) connected by a 14 residue-long flexible linker that lacks electron density and thus appears to be disordered in the crystal (Figure 1A).
The C domain was then added through extension of the N-domain C-terminal α helix, with the interdomain linker (disordered in the crystals) modeled in an α-helical conformation.
Cross-references: PDB:2OUG
Protein: DP03913 (UniProt P0AFW0)
Region: residues 101	to 114
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit contains two molecules of RfaH (see Figure S1 in the Supplemental Data available with this article online); each protomer consists of two domains (N and C terminal) connected by a 14 residue-long flexible linker that lacks electron density and thus appears to be disordered in the crystal (Figure 1A).
The overall structural similarity between RfaH and NusG might be extended to the long flexible linkers connecting the C and N domains.
The C domain was then added through extension of the N-domain C-terminal α helix, with the interdomain linker (disordered in the crystals) modeled in an α-helical conformation.
Cross-references: PDB:2OUG
Protein: DP03914 (UniProt G0SCF1)
Region: residues 31	to 88
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary chemical shift analysis (Fig. 4 C) clearly indicates an α-helical structure for residues 1–30 (the SAH region) and a nascent α-helix for residues 50–64 (the H2 region). Other residues with secondary chemical shift values close to zero are intrinsically disordered.
Three-bond HN-Hα scalar coupling constants (3JHN-Hα) for IC88 (Fig. 4 D) are in the range of 4–6 Hz for residues 1–30, which implies that this region has an α-helical secondary structure. The remaining residues have coupling values that are, for the most part, between 6 and 8 Hz, which is consistent with these residues lacking a fixed secondary structure. 
Both the 3JHN-Hα and the 1DHN coupling values support our prediction that the H2 region forms a nascent, rather than a fully formed, α-helix.
Cross-references: PDB:6PQT
Protein: DP03914 (UniProt G0SCF1)
Region: residues 31	to 88
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
In comparison, the thermogram for IC35 binding to p150ABC (Fig. 7 A, middle) showed that removing H2 and the disordered linker regions surrounding it (residues 30–50 and 60–88) drastically diminished the second step.
Protein: DP03914 (UniProt G0SCF1)
Region: residues 50	to 64
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An NMR titration of 15N-labeled IC37–88 with unlabeled p150ABC (Fig. 7 D) shows a complete loss of signal for the H2 region and that signal for the linker regions diminishes depending on how close the linker residues are to the H2 region. This confirms that the H2 region directly interacts with p150ABC and strongly suggests that reduced peak volumes for residues in the linker regions (as seen in Figs. 6 C and ​and77 D) are a result of the reduced mobility of these residues due to their proximity to regions that bind p150ABC rather than due to a direct interaction between these residues and p150ABC.
Protein: DP03914 (UniProt G0SCF1)
Region: residues 77	to 161
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The limited chemical shift dispersion at 10°C (Figure 4B), along with appearance of the majority of the peaks in the CLEANEX experiment at this temperature (Figure 4C), indicates that the peaks observed in the spectra are for the disordered regions of IC1-260.
Assigned residues are in black in the sequence above the plot (and unassigned residues in gray); all assigned residues are from disordered regions of IC1-260.
Protein: DP03915 (UniProt P22108)
Region: residues 53	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the apo-Apa2 model, residues Lys53–Glu65 and Lys134–Thr139 in molecule A and Lys53–Lys63 in molecule B are missing due to their poor electron density.
Notably, the missing residues (Lys53–Glu65) from three structures of Apa2 were probably located across the Ap4A-binding cleft, suggesting that these residues might be adjacent to the Ap4A entrance tunnel and thus are relatively flexible.
Residues 53-63 are disordered in both the apo-Apa2 and Apa2-AMP structures.
Cross-references: PDB:4I5W
PDB:4I5T
Protein: DP03916 (UniProt Q3E7B7)
Region: residues 1	to 35
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The limited dispersion of the 1 H–15 N HSQC peaks, especially in the 1 H dimension (between 7.6 and 8.5 ppm), indicated at least part of the ScSERF segments was in an unfolded state in the NMR experimental buffer condition (20mM phosphate, 50mM NaCl, pH 6.5). In a next step, secondary chemical shift deviations were calculated and are shown in Fig. 3. Consistent with the dispersion of peaks in 1 H dimension, the N terminal segments of residues 1–35 yielded a secondary chemical shift deviation close to 0, corresponding to a random coil structure. However, the segment of residues spanning 36–65 showed a clear helical secondary structure propensity based on its consecutive positive secondary chemical shift deviation.
Cross-references: BMRB:51051
BMRB:51287
Protein: DP03917 (UniProt Q14011)
Region: residues 90	to 172
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The IDD of hnRNP A18 (aa. 90–172) contained chemical shift values consistent with random coil and did not suggest strong secondary structural characteristics at any location. In accordance with chemical shifts suggestive of random coil, the Random Coil Index (RCI) order parameter (RCI-S2) values for the IDD were lower than the values for the RRM. This analyses suggests the backbone of the IDD is significantly more flexible than the backbone of the RRM.
Cross-references: BMRB:51517
Protein: DP03918 (UniProt O39946)
Region: residues 61	to 91
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 2D [1H–15N]-BTROSY-HSQC spectrum of 15N-13C-labelled SΔ60 is shown in Fig.1. The spectrum displays a high quality, with a dispersion corresponding to a partially disordered protein.
Similarly, the residues of the disordered parts (N-ter residues 58–91 and C-ter residues 150–194) show strong shielding effects with increasing temperature, meaning that their bond lengths are more sensitive to temperature changes, and thus that these regions are less involved in hydrogen bonds.
Although the authors mention residue 58 as the start of the disordered region, that is still part of the five residues remaining from the GST tag after cleavage. The  first residue that is part of the actual protein sequence is residue 61.
Cross-references: BMRB:51340
Protein: DP03918 (UniProt O39946)
Region: residues 150	to 194
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 2D [1H–15N]-BTROSY-HSQC spectrum of 15N-13C-labelled SΔ60 is shown in Fig.1. The spectrum displays a high quality, with a dispersion corresponding to a partially disordered protein.
Similarly, the residues of the disordered parts (N-ter residues 58–91 and C-ter residues 150–194) show strong shielding effects with increasing temperature, meaning that their bond lengths are more sensitive to temperature changes, and thus that these regions are less involved in hydrogen bonds.
Cross-references: BMRB:51340
Protein: DP03919 (UniProt O15151)
Region: residues 181	to 300
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The chemical shift data are consistent with a scenario where the AD is an intrinsically disordered region, as the sequence has significant random-coil propensity.
Cross-references: BMRB:51090
Protein: DP03919 (UniProt O15151)
Region: residues 181	to 300
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum exhibits narrow dispersion in the proton dimension (Fig. 3). This is characteristic of an intrinsically disordered protein, with most resonances occupying the central part of the spectrum.
Cross-references: BMRB:51090
Protein: DP03919 (UniProt O15151)
Region: residues 181	to 300
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectra of intrinsically disordered proteins typically have a negative band at ~ 200 nm and an ellipticity close to zero at 222 nm, features that are distinct from folded proteins and which make it possible to identify partially or fully disordered proteins. Consistent with this, the CD spectrum of the AD exhibited a strong negative band at ~ 202 nm, suggesting that the AD contains a significant proportion of disordered content.
Protein: DP03920 (UniProt D8SB57)
Region: residues 39	to 52
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Furthermore, the linker region between the two fingers in the TZF domain of spikemoss is unstructured (residues D39 - E52), in both the presence and absence of RNA, similar to the linker region in the TIS11d-RNA complex (Fig. 2).
Cross-references: BMRB:51209
BMRB:51210
Protein: DP03921 (UniProt A5Y0M2)
Region: residues 92	to 112
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of Cα and Cβ chemical shifts indicated that TuSp2-RP consists of at least six α-helices (Fig. 2) and the first 37-residues (including the His-tag) exist in a random coil form.
Excluding the first 16 residues of the N-terminal His-tag and the four proline residues from the 158-residue recombinant TuSp2-RP sequence, 132 out of a total of 138 residues (~ 96%) were assigned in the 1H–15N HSQC spectrum.
The authors specify that the construct has a 16 residue N-terminal His tag, then they claim that the first 37-residues (including the His-tag) are disordered, therefore the first 21 residues of the protein construct are disordered that is residues 92-112 of the UniProt sequence.
Cross-references: BMRB:36395
Protein: DP03922 (UniProt Q13586)
Region: residues 395	to 404
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The main structural features are a short (single turn) α-helix at the N-terminus followed by approximately 10 amino acids in a disordered loop region (H395 to D404) and a longer (ca. 6 turn) α-helix (V405 to L427). 
In the monomeric state, a short disordered segment (H395 to D404) interrupts the α-helix close to the N-terminus.
Cross-references: BMRB:50683
Protein: DP03923 (UniProt Q9R825)
Region: residues 31	to 48
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The longest loop (res. G38 – G55) of B. afzelii DbpA contains a small approx. one-turn alpha helix just like DbpA from B. burgdorferi s.s., whereas in the more sequentially related B. garinii DbpA one found a long alpha helix in the same place.
The authors apply an 8 aa long His tag in place of the initiating Met residue, therefore their numbering is shifted by 7 residues. G38-G55 corresponds to G31-G48 in the UniProt sequence. 
Besides the statement of the authors that the region is a loop, there are also markedly decreased RCI S2 values, R1/R2 values and N{H} NOE values in this region as shown in Figure 2b and c, especially between residues 33 and 48.
Cross-references: BMRB:50751