LiteFold/DisProt huggingface dataset:
Protein: DP02210 (UniProt Q03519)
Region: residues 1	to 129
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No density was observed for either the C-terminal 33 residues of ICP47 or the two TMD0s, indicating these regions are flexible in this conformation.
Cross-references: PDB:5U1D
Protein: DP02212 (UniProt P05769)
Region: residues 1442	to 1465
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As observed for the DENV NS2B-NS3pro structure, in the absence of a substrate, the MVEV NS2B region beyond residue 69 is disordered. Upon the addition of a substrate, the C-terminal part of NS2B undergoes a dramatic conformational change, wrapping around the C-terminal barrel and forming a stabilizing β hairpin that inserts into the active site (2, 19, 47).
Cross-references: PDB:2WV9
Protein: DP02212 (UniProt P05769)
Region: residues 1504	to 1520
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Regarding electron density, a total number of 580 out of 618 residues of full-length NS3 are well defined, together with 21 residues out of 45 of NS2B45. The 9 residues of the nonapeptide linker, 24 residues at the C terminus of the NS2B cofactor, 18 residues at the N terminus of the protease domain, and 7 residues in the linker region between protease and helicase are missing from the refined model.
Cross-references: PDB:2WV9
Protein: DP02212 (UniProt P05769)
Region: residues 2085	to 2095
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows disorder in the NS3 region 2085-2095 .
Cross-references: PDB:2WV9
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
MUT-16 has a short IDR near the N-terminus (first ~100 amino acids) and a much longer IDR comprising approximately 60% of the protein (Fig 1A). In total, more than 70% of the protein is predicted to be unstructured.
We also observed that the MUT-16 protein is highly prone to degradation during the immunoprecipitation procedure. While full-length MUT-16 could be observed in most lanes, we also could detect multiple degradation products, with a prominent product of ~70kD in most lanes (S5 Fig). We did not observe substantial degradation with other proteins we worked with and suspect the highly disordered nature of MUT-16 may leave it more exposed to proteases during the immunoprecipitation procedure.
This region is ~70% disordered, but contains the structured L region that is also key to the formation of Mutator foci.
The IUPred analysis in combination to the high degree of degradation highlight the flexibility and high solvent exposure of the protein. The curator resorted to the deletion experiments and to MobiDB for further structural information to determine the IDRs boundaries.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 366	to 946
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
MUT-16 has a short IDR near the N-terminus (first ~100 amino acids) and a much longer IDR comprising approximately 60% of the protein (Fig 1A). In total, more than 70% of the protein is predicted to be unstructured.
We also observed that the MUT-16 protein is highly prone to degradation during the immunoprecipitation procedure. While full-length MUT-16 could be observed in most lanes, we also could detect multiple degradation products, with a prominent product of ~70kD in most lanes (S5 Fig). We did not observe substantial degradation with other proteins we worked with and suspect the highly disordered nature of MUT-16 may leave it more exposed to proteases during the immunoprecipitation procedure.
This region is ~70% disordered, but contains the structured L region that is also key to the formation of Mutator foci.
The IUPred analysis in combination to the high degree of degradation highlight the flexibility and high solvent exposure of the protein. The curator resorted to the deletion experiments and to MobiDB for further structural information to determine the IDRs boundaries. The authors refer to L region to the 947-1033 residues.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 773	to 884
Annotation: non-membrane-bounded organelle assembly (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
In contrast, ΔJ, ΔK, and ΔL displayed severely disrupted foci, though the overall expression of cytoplasmic MUT-16 was not reduced (Fig 3A and 3D).
Together, these data indicate that C-terminal region of MUT-16 (J, K, and L) contains a region essential for foci formation.
Mutator focus is a type of punctate focus. Mutator foci are required for RNA interference (RNAi). Additionally, the authors refer to J as the 773-884 region, and K as the 885-945 region.
This finding suggests that isolated stretches of disordered amino acids are not sufficient to mediate phase separation, but require the neighboring protein environment to promote Mutator foci formation.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 885	to 945
Annotation: non-membrane-bounded organelle assembly (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
In contrast, ΔJ, ΔK, and ΔL displayed severely disrupted foci, though the overall expression of cytoplasmic MUT-16 was not reduced (Fig 3A and 3D).
Together, these data indicate that C-terminal region of MUT-16 (J, K, and L) contains a region essential for foci formation.
Mutator focus is a type of punctate focus. Mutator foci are required for RNA interference (RNAi). Additionally, the authors refer to J as the 773-884 region, and K as the 885-945 region.
This finding suggests that isolated stretches of disordered amino acids are not sufficient to mediate phase separation, but require the neighboring protein environment to promote Mutator foci formation.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 484	to 569
Annotation: posttranscriptional gene silencing (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Surprisingly, our RNAi assays revealed that only mut-16 deletions ΔC, ΔF, ΔH-I, and ΔL have a significant impact on somatic RNAi (Fig 2A and 2B). The remaining deletions had only mild or no RNAi defect. In contrast, all deletions in mut-16 had defects in germline RNAi, though deletions in ΔA and ΔG had more modest effects (Fig 2C). These data reveal that the majority of the MUT-16 protein is necessary for robust germline RNAi. In contrast, some regions of MUT-16 are dispensable for the response to at least some somatic RNAi clones, suggesting that the soma may be more resilient to mild perturbations in MUT-16.
The authors refer to F as the 484-569 region, and H-I as the 632-772 region.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 632	to 772
Annotation: posttranscriptional gene silencing (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Surprisingly, our RNAi assays revealed that only mut-16 deletions ΔC, ΔF, ΔH-I, and ΔL have a significant impact on somatic RNAi (Fig 2A and 2B). The remaining deletions had only mild or no RNAi defect. In contrast, all deletions in mut-16 had defects in germline RNAi, though deletions in ΔA and ΔG had more modest effects (Fig 2C). These data reveal that the majority of the MUT-16 protein is necessary for robust germline RNAi. In contrast, some regions of MUT-16 are dispensable for the response to at least some somatic RNAi clones, suggesting that the soma may be more resilient to mild perturbations in MUT-16.
The authors refer to F as the 484-569 region, and H-I as the 632-772 region.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 484	to 772
Annotation: RNA polymerase binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Only the ΔF mutant completely disrupted the interaction between MUT-16 and RRF-1, though the amount of RRF-1 immunoprecipitated by the ΔB, ΔC, and ΔG mutants was modestly reduced relative to full-length MUT-16 (Fig 4F). 
In particular, region F recruits the RdRP protein RRF-1 and the H-I region recruits the exonuclease MUT-7 through its interaction with RDE-2. 
The authors refer to F as the 484-569 region.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 484	to 772
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
In contrast, RDE-2 fails to localize to Mutator foci in the ΔH-I deletion, and RRF-1 is at least partially disrupted in ΔB, ΔC, ΔF, and ΔG mutants (Fig 4A and S4 Fig). 
In particular, region F recruits the RdRP protein RRF-1 and the H-I region recruits the exonuclease MUT-7 through its interaction with RDE-2. 
The authors refer to H-I as the 632-772 region.
Protein: DP02216 (UniProt Q9U3S5)
Region: residues 773	to 945
Annotation: mutator focus (Cellular component)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Surprisingly, ΔE-I, which removes 387 amino acids (~37% of the protein) and encompasses a substantial portion of the IDR, does not affect MUT-16 localization, indicating that a large portion of the IDR is dispensable for foci formation. In contrast, ΔE-K does disrupt MUT-16 localization, which is not unexpected given that it includes J and K regions, which individually disrupted foci formation.
The authors describe how the deletion of the J-K region (773-945) leads to the mis-localization of the protein outside the Mutator focus.
Protein: DP02220 (UniProt P32521)
Region: residues 1191	to 1480
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In general, disordered regions do not pellet after heating while structured regions tend to unfold upon boiling and
aggregate upon cooling, causing them to be found in the pellet after centrifugation. ... In contrast, the C-terminal fragment (His6-Pan1 1191–1480) did not pellet after boiling, consistent with the unstructured prediction from the PONDR analysis.
Protein: DP02220 (UniProt P32521)
Region: residues 1191	to 1480
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The Pan1 N-terminal fragment (amino acids 230–700) exhibited the typical CD spectrum for a-helices, with peaks at 222 and 208 nm, while the CD spectrum of the C-terminus (amino acids 1191–1480) indicated that this region is mostly random coil.
Protein: DP02224 (UniProt P29375)
Region: residues 184	to 360
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained amino acids 12–183 and 361–785, with remaining amino acid residues disordered. Relatively strong but discontinuous difference electron density for a short stretch of amino acids (approximately ten residues) beyond residue 183 exists but was not sufficient to convincingly set the registration of the chain.
Cross-references: PDB:5CEH
Protein: DP02224 (UniProt P29375)
Region: residues 184	to 360
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region also corresponds to the KDM5A PHD1 domain, which is disordered in this structure too as in 5CEH
Cross-references: PDB:5K4L
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 172	to 338
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Although the spectra of the six recombinant proteins showed different characteristics, they all had a minimum around 200 nm and only slightly negative ellipticities at 222 nm (Figure 4a). Both the [θ]222 and [θ]200 values suggested that histidine–NTL8 (156–335), ANAC013 (161–498), NAP (162–268) and ANAC019 (163–317) are similar, populating pre-molten globule like ensembles, whereas the values for histidine–SOG1 (210–449) and ANAC046 (172–338) suggest more random coil-like ensembles.
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 319	to 338
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Similar to DREB2A(255–272), free ANAC013(254–274) and ANAC046(319–338) had poorly dispersed HSQC spectra (Fig. 7, B and C, black spectra), and ΔδCα values close to zero (Fig. 7, E and F, top figures) again confirming a lack of preformed structure.
In support of this, no indications of transiently formed structure were apparent from the secondary Cα chemical shifts (Fig. 7F, top figure) or AGADIR predictions (Fig. 5A) for ANAC046.
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 319	to 338
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Comparison of the HSQC spectra of free and bound ANAC013(254–274) and ANAC046(319–338) confirmed their interaction with RCD1-RST(499–572) (Fig. 7, B and C), but in contrast to those of DREB2A(255–272), the dispersion in the proton dimension appeared immediately unaffected.
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 319	to 338
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The ANAC046(319–338)·RCD1-RST(499–572) complex had an overall α-helical content of 38%, compared with 34% in the theoretical complex. However, in this case a shift toward a lower wavelength in the complex was observed (Fig. 6D). Together, the results suggested that complex formation involving ANAC046(319–338) and ANAC013(254–274) resulted in structure induction, although to a lower degree than that of the DREB2A(255–272)·RCD1-RST(499–572) complex.
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 315	to 338
Annotation: calcium ion binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Here, based on the CSPs, we observed binding in the region of M315 to S338, indicating a localized C-terminal interaction occurring at the same binding site at which ANAC046 interacts with radical induced cell death1 (RCD1) [43].
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 315	to 338
Annotation: calcium ion binding (Molecular function)
Evidence: small molecule detection assay evidence used in manual assertion
Supporting statements:
Here, based on the CSPs, we observed binding in the region of M315 to S338, indicating a localized C-terminal interaction occurring at the same binding site at which ANAC046 interacts with radical induced cell death1 (RCD1) [43].
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 172	to 338
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
ANAC046172-338 narrow secondary chemical shifts dispersion (confined in the region 8.0 to 8.5 ppm) shown in the Supplementary figures and the BMRB file, indicates this region is disordered.
Cross-references: BMRB:51033
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 172	to 338
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Although the relative migration pattern of the recombinant proteins by SDS/PAGE was in accordance with their relative molecular mass values [NAP (162–268): 15.0 kDa; ANAC019 (163–317): 17.2 kDa; ANAC046 (172–338): 18.2 kDa; histidine–NTL8 (156–335): 20.3 kDa; histidine–SOG (210–449): 29.0 kDa; ANAC013 (161–498): 37.5 kDa], they displayed slow migration during SDS/PAGE compared with standard globular proteins, which is in accordance with their ID nature and previous analysis of two NAC TRDs [39].
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 172	to 338
Annotation: pre-molten globule (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
This aspect was analysed by size-exclusion chromatography for the four untagged NAC TRDs. The hydrodynamic radii (Stokes radii) of ANAC046 (172–338), NAP (162–268) and ANAC019 (163–317) corresponded to pre-molten globule states, whereasANAC013 (161–498) had a more compact structure consistent with its disorder profile (Figures 1d and 3).
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 315	to 338
Annotation: transcription regulator activator activity (Molecular function)
Evidence: beta galactosidase functional complementation evidence used in manual assertion
Supporting statements:
After demonstrating the ability of full-length ANAC046 and its TRD to activate transcription, analysis of C-terminally truncated versions of these suggested the importance of the MoRF region for the activity (Figure 7c). This was supported by the ability of ANAC046 (315–338) to activate transcription.
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 315	to 338
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
As expected, the RST domain of RCD1 interacted with both full-length ANAC013 and ANAC046 and their TRDs (Figures 7b and 7c), whereas no interaction was detected with NAP (Figure 7a) [27].
C-terminal truncations were also analysed for their ability to interact with DBD–RCD1 (498-573). This suggested that residues 205–299 of ANAC013 and that the very C-terminal MoRF region of ANAC046 were responsible for the interactions (Figures 7b–7c).
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 172	to 338
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A slight change of the absolute minimum towards a lower wavelength for the complex compared with the theoretical complex, obtained by adding the individualANAC046 (172–338) and histidine–RCD1–RST (487–589) spectra, suggested that complex formation does not involve folding, but is suggestive of unfolding.
Protein: DP02225 (UniProt Q9SQQ6)
Region: residues 328	to 338
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The affinities of the ANAC013 TRD, ANAC013 (161–498) and the ANAC046 TRD, ANAC046 (172–338), for the RST domain, RCD1–RST (499–572), was approximately the same with Kd values of 537 nM and 609 nM respectively (Figures 8a and 8b; Table 1).
Binding to the synthetic peptidesANAC046 (319–338) andANAC046 (328–338)was also analysed. Both span the MoRF region (Figure 5).
Binding of these peptides to RCD1–RST (499–572) showed approximately the same Kd as was obtained for binding of ANAC046 (172–338) to RST.
Protein: DP02226 (UniProt P24385)
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:
Cyclin D1 is known to contain 2 Rb binding sites (17) comprised of an N-terminal LxCxE consensus motif and a peptide recruitment site. The cyclin D1 structure exhibits N-terminal disorder, so the LxCxE motif cannot be visualized.
Cross-references: PDB:2W96
Protein: DP02226 (UniProt P24385)
Region: residues 256	to 295
Annotation: disorder (Structural state)
Evidence: author inference used in manual assertion
Supporting statements:
The predictors agree that most of the cyclin D1 sequence encodes for a structured protein (aa1-aa255, corresponding to a carboxyl-terminal and an amino-terminal domain), whereas the carboxyl-terminal 40 residues (aa256-aa295) have a strong tendency to be intrinsically disordered. Considering the training sets of the predictors relying on examples of IDPs/IDRs, we can be sure that this region does not fluctuate around an equilibrium conformation (that is, it is not “flexible”). Rather it is disordered and can assume a broad ensemble of conformations most appropriate for potentially adapting to diverse binding partners. This is particularly true for the E-rich region. The last carboxyl-terminal 15 residues appear as a down-peak on the disordered pattern (Fig. 4A) with alternating acidic and aliphatic residues, and its behavior of predicted disorder and local hydrophobicity is characteristic of IDP binding motifs. In agreement, this region gives a very strong signal by the ANCHOR predictor (Fig. 4A) developed to recognize specific protein recognition sites embedded in IDPs/IDRs [48].
Disorder tendency and disordered binding site prediction. PRDos (blue), IUPred long (maroon), PONDR (orange) predictions show that the carboxy-terminal 40 residues (aa 256 - aa295) have a strong tendency to be intrinsically disordered, whereas ANCHOR (black) suggests that last 15 amino acids contain a protein-protein interaction site.
Protein: DP02227 (UniProt Q02821)
Region: residues 510	to 530
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystal diffracting was obtained with a shorter fragment, comprising residues 88-530.
"The refined model comprises residues 89–509 of karyopherin α, 140 water molecules, and a cobalt ion, while the 20 carboxy-terminal residues are disordered and not modeled."
Protein: DP02231 (UniProt Q99958)
Region: residues 134	to 144
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
"the region running from residue 66 to 76 are significantly less ordered."
Cross-references: PDB:1D5V
Protein: DP02233 (UniProt Q13547)
Region: residues 377	to 482
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
HDAC is crystallised in complex with the MTA1 protein, and the C-terminal region of HDAC remains disordered in the complex.
Cross-references: PDB:4BKX
Protein: DP02233 (UniProt Q13547)
Region: residues 377	to 482
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region contains an IxCxE motif (414-420) that binds to the Retinoblastoma tumor suppressor (pRb)
Protein: DP02234 (UniProt P08476)
Region: residues 359	to 386
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For activin A, residues 49–76 that form the canonical TGF-β ‘wrist’ region are disordered in both crystal forms, similar to the TGF-β3:TβRII complex.
Cross-references: pdb:1nyu
Protein: DP02247 (UniProt P10721)
Region: residues 544	to 565
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of activated c-Kit kinase was determined (residues 544–935). This structure contains two c-Kit enzyme molecules in the asymmetric unit and clear electron density was observed for residues 566–935.
"The amino-terminal ∼20 amino acid residues of both enzymes are disordered"
Cross-references: PDB:1PKG