LiteFold/DisProt huggingface dataset:
Protein: DP04284 (UniProt Q8TDX7)
Region: residues 190	to 195
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
Activated Nercc1 directly catalyzes the phosphorylation of Nek6 Ser206 (and of the equivalent site, Ser195, in Nek7) and generates a robust activation of wild type Nek6/7 in vitro. 3)
Protein: DP04284 (UniProt Q8TDX7)
Region: residues 182	to 195
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 20–300 of Nek7Y97F were modelled with the exception of the activation loop residues 182–195 (chain A) and 181–199 (chain B), which were disordered.
Cross-references: PDB:5DE2
Protein: DP04284 (UniProt Q8TDX7)
Region: residues 1	to 19
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density for this region.
Cross-references: PDB:2WQM
Protein: DP04284 (UniProt Q8TDX7)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density for this region.
Cross-references: PDB:2WQM
Protein: DP04284 (UniProt Q8TDX7)
Region: residues 190	to 195
Annotation: regulation of kinase activity (Biological process)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 4C, Nercc1 catalyzes the phosphorylation of Nek6 (Ser206) and the equivalent site on Nek7 (Ser195), resulting in a 20–25-fold activation of Nek6/7 kinase activity.
Protein: DP04285 (UniProt Q9UK59)
Region: residues 394	to 544
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The order/disorder predictor PONDR uses the relative frequency of charged and hydrophobic residues to forecast the presence of disordered regions (29), and PONDR clearly predicted that the C-terminal ∼150 aa of Dbr1 are unstructured (Fig. 1B). Consistent with this PONDR prediction, unstructured polypeptide is present in the C-terminal domain of an hDbr1 Alpha-Fold model (Fig. 1C) (30, 31).
The amide and aliphatic proton regions were indistinguishable for the two samples. We concluded that hDbr1 had the same folded state when expressed in prokaryotic or eukaryotic cells and that the presence of the random coil was not an artifact of heterologous expression in prokaryotic cells. A circular dichroism spectra of E. coli expressed hDbr1 is presented in Fig. S1B.
Protein: DP04285 (UniProt Q9UK59)
Region: residues 503	to 544
Annotation: protein stabilization (Biological process)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Full-length Dbr1 was monodisperse, with a narrow distribution of S-values centered around 4.3 (Fig. 2A). Dbr1-502 and Dbr1-399 showed considerable aggregation, with ∼20% of the samples sedimenting at very large S-values.
The disordered C terminus stabilizes Dbr1 but is not required for activity
Protein: DP04285 (UniProt Q9UK59)
Region: residues 394	to 544
Annotation: flexible C-terminal tail (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The order/disorder predictor PONDR uses the relative frequency of charged and hydrophobic residues to forecast the presence of disordered regions (29), and PONDR clearly predicted that the C-terminal ∼150 aa of Dbr1 are unstructured (Fig. 1B). Consistent with this PONDR prediction, unstructured polypeptide is present in the C-terminal domain of an hDbr1 Alpha-Fold model (Fig. 1C) (30, 31).
The amide and aliphatic proton regions were indistinguishable for the two samples. We concluded that hDbr1 had the same folded state when expressed in prokaryotic or eukaryotic cells and that the presence of the random coil was not an artifact of heterologous expression in prokaryotic cells. A circular dichroism spectra of E. coli expressed hDbr1 is presented in Fig. S1B.
Protein: DP04286 (UniProt Q8TAP9)
Region: residues 1	to 135
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
We observed a drop in the amide region (8.2 ppm) at acidic pH (pH 4.5 versus 7.4), suggesting a collapse of structure at low pH. Circular dichroism of TTDN1 (pH 7.4) verified this helical content, with a minima around 220 nm (Fig. S1B). A predicted structure of TTDN1 also has short helical regions (Fig. S1C) (30, 31).
AlphaFold prediction shows the region 136-159 is the one 
that is contributing to the structured component seen in the experimental approaches.
Protein: DP04286 (UniProt Q8TAP9)
Region: residues 160	to 179
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
We observed a drop in the amide region (8.2 ppm) at acidic pH (pH 4.5 versus 7.4), suggesting a collapse of structure at low pH. Circular dichroism of TTDN1 (pH 7.4) verified this helical content, with a minima around 220 nm (Fig. S1B). A predicted structure of TTDN1 also has short helical regions (Fig. S1C) (30, 31).
AlphaFold prediction shows the region 136-159 is the one 
that is contributing to the structured component seen in the experimental approaches.
Protein: DP04287 (UniProt O14907)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues M1−T10 and A113−S124 are not shown because they are highly disordered and have chemical shifts perturbations of <0.05 ppm. 
Cross-references: BMRB:17254
PDB:2L4S
Protein: DP04287 (UniProt O14907)
Region: residues 113	to 124
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues M1−T10 and A113−S124 are not shown because they are highly disordered and have chemical shifts perturbations of <0.05 ppm. 
Cross-references: BMRB:17254
PDB:2L4S
Protein: DP04288 (UniProt P29066)
Region: residues 360	to 382
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for residues 334–338 and 360–382 in chain A and chain B, respectively.
Cross-references: PDB:8HSV
Protein: DP04290 (UniProt Q9V6Q2)
Region: residues 101	to 146
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No observed electron density for this region.
Cross-references: PDB:6XWT
Protein: DP04290 (UniProt Q9V6Q2)
Region: residues 1	to 131
Annotation: disorder (Structural state)
Evidence: intrinsic disorder prediction evidence used in manual assertion
Supporting statements:
This region is classified as intrinsically disordered, based on the disorder consensus prediction from the corresponding MobiDB entry.
Protein: DP04294 (UniProt I1KDC1)
Region: residues 80	to 305
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectra of GmMBD10c in water showed a deep minimum near 198 nm, which is indicative of a mostly disordered structure.
In water, GmMBD10c is largely disordered, with several disordered regions predicted in the region comprising aa 80–305.
The combination of experimental evidence and a variety of disorder predictors used by the authors allow us to determine 80-350 as the IDR's boundaries.
Protein: DP04294 (UniProt I1KDC1)
Region: residues 80	to 305
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
To confirm the disordered structure of GmMBD10c, a 1H NMR spectrum was obtained and analyzed. The peaks in the amide region of the spectrum (from 6.6 to 7.8 ppm) are not well dispersed, similar to that of soybean LOC protein, another partially unstructured protein [29].Therefore, we conclude that GmMBD10c is partially disordered in aqueous medium (Figure 4).
In water, GmMBD10c is largely disordered, with several disordered regions predicted in the region comprising aa 80–305.
The combination of experimental evidence and a variety of disorder predictors used by the authors allow us to determine 80-350 as the IDR's boundaries.
Protein: DP04295 (UniProt Q9Y572)
Region: residues 387	to 518
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N heteronuclear single quantum coherence (HSQC) spectra recorded on these protein samples, whose final concentrations are in the range 18 to 20 μM, revealed the typical pattern of disordered proteins.
Protein: DP04295 (UniProt Q9Y572)
Region: residues 387	to 518
Annotation: amyloid fibril formation (Biological process)
Evidence: thioflavin T based fluorescence spectroscopy evidence
Supporting statements:
According to thioflavin T (ThT) assays, the broadening and loss of intensity observed upon raising the pH is consistent with the assembly of amyloid fibrils when the pH is raised to 6.5 from pH 4.0 (Fig. 2B).
Protein: DP04295 (UniProt Q9Y572)
Region: residues 430	to 465
Annotation: identical protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In order to establish whether monomers use this region preceding the RHIM to directly interact with the fibril surface in the amyloid-bound state, we prepared a 15N-labeled RIPK3 (387–518) sample to obtain the difference in transverse relaxation rates, ΔR2, under assembling (at 180 μM) and nonassembling (at 18 μM) conditions (Figs. 3F and S5).
Under these conditions, the resulting ΔR2 (i.e., R2 at 180 μM minus R2 at 18 μM) identifies which residues in the monomer establish specific contacts with the fibril during the dynamic equilibrium between unbound and amyloid-bound monomers (Fig. 3F).
More intriguing, our data reveal that in addition to the RHIM, its preceding ca. 20-residue stretch readily established contacts with the fibril surface in the assembled state.
Protein: DP04295 (UniProt Q9Y572)
Region: residues 388	to 447
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
Cross-references: EMDB:30622
PDB:7DA4
Protein: DP04295 (UniProt Q9Y572)
Region: residues 470	to 518
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
Cross-references: EMDB:30622
PDB:7DA4
Protein: DP04295 (UniProt Q9Y572)
Region: residues 476	to 518
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
Cross-references: PDB:7DAC
Protein: DP04295 (UniProt Q9Y572)
Region: residues 418	to 446
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
Cross-references: PDB:7DAC
Protein: DP04295 (UniProt Q9Y572)
Region: residues 447	to 475
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
Only residues from P448 to P475 gave ssNMR signals, indicating the location of the rigid fibril core (chemical shift assignment was shown in SI Appendix, Table S1).
The RIPK3-CTD fibril core is highly ordered and compact featuring an S-shaped architecture, consisting of three β-strands (strands 1 through 3) stacking along the fibril axis in a parallel and in-register fashion (Fig. 3D).
Cross-references: PDB:7DAC
Protein: DP04295 (UniProt Q9Y572)
Region: residues 447	to 475
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
Only residues from P448 to P475 gave ssNMR signals, indicating the location of the rigid fibril core (chemical shift assignment was shown in SI Appendix, Table S1).
The RIPK3-CTD fibril core is highly ordered and compact featuring an S-shaped architecture, consisting of three β-strands (strands 1 through 3) stacking along the fibril axis in a parallel and in-register fashion (Fig. 3D).
Upon fibril formation this region gets compact and ordered as it act as the core of the fibrils.
Cross-references: PDB:7DAC
Protein: DP04295 (UniProt Q9Y572)
Region: residues 448	to 469
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
The RIPK3-CTD fibril core is highly ordered and compact featuring an S-shaped architecture, consisting of three β-strands (strands 1 through 3) stacking along the fibril axis in a parallel and in-register fashion (Fig. 3D).
Upon fibril formation this region gets compact and ordered as it act as the core of the fibrils.
Cross-references: PDB:7DA4
EMDB:30622
Protein: DP04295 (UniProt Q9Y572)
Region: residues 448	to 469
Annotation: order (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ssNMR and cryo-EM structures show that the core of the RIPK3-CTD fibril is very small, consisting of only ∼20 residues out of a total of over 100 residues of RIPK3-CTD (Fig. 3A). The rest of the residues in the CTD remain flexible and are invisible by either cryo-EM or ssNMR.
The RIPK3-CTD fibril core is highly ordered and compact featuring an S-shaped architecture, consisting of three β-strands (strands 1 through 3) stacking along the fibril axis in a parallel and in-register fashion (Fig. 3D).
Upon fibril formation this region gets compact and ordered as it act as the core of the fibrils.
Cross-references: PDB:7DA4
EMDB:30622
Protein: DP04295 (UniProt Q9Y572)
Region: residues 388	to 518
Annotation: amyloid fibril formation (Biological process)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structure reveals that the RIPK3-CTD fibril features a small fibril pitch of ∼23 nm and a large twist angle of −7.53° (Fig. 2C and SI Appendix, Fig. S3C). 
Cross-references: PDB:7DA4
EMDB:30622
Protein: DP04295 (UniProt Q9Y572)
Region: residues 388	to 518
Annotation: ripoptosome (Cellular component)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we present the high-resolution solid-state nuclear magnetic resonance (SSNMR) structure of the RIPK1-RIPK3 amyloidal signaling complex, featuring sequential and specific stacking to form a hetero-amyloid serpentine fold, stabilized by hydrophobic packing and enriched with interactions along the fibrillar axis such as Asn and Gln ladders, Tyr stacking, and an unusual Cys-Ser ladder.
Cross-references: PDB:5V7Z
Protein: DP04295 (UniProt Q9Y572)
Region: residues 448	to 462
Annotation: protein serine/threonine kinase binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we present the high-resolution solid-state nuclear magnetic resonance (SSNMR) structure of the RIPK1-RIPK3 amyloidal signaling complex, featuring sequential and specific stacking to form a hetero-amyloid serpentine fold, stabilized by hydrophobic packing and enriched with interactions along the fibrillar axis such as Asn and Gln ladders, Tyr stacking, and an unusual Cys-Ser ladder.
Cross-references: PDB:5V7Z
Protein: DP04295 (UniProt Q9Y572)
Region: residues 446	to 464
Annotation: protein serine/threonine kinase binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
His-tag pull-down experiments of the coexpression constructs showed that the interaction was retained, even when RIP1 was only 31 residues (525–555) and RIP3 was only 19 residues (446–464) in length (Figures 3A, S3A, and S3B).
Protein: DP04295 (UniProt Q9Y572)
Region: residues 388	to 518
Annotation: amyloid fibril formation (Biological process)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
(E) Superimposed Fourier transform infrared spectra of RIP/RIP3-RHIM (magenta) and the I539D mutant of RIP1 (cyan). Only the WT RIP1/RIP3 complexes, not the RHIM mutant, showed the amide I’ maxima at 1,623 cm−1 (dashed vertical red line), which is characteristic of β-amyloid.
Protein: DP04295 (UniProt Q9Y572)
Region: residues 388	to 518
Annotation: ripoptosome assembly involved in necroptotic process (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Clustering of RIP1 and RIP3 into punctate-like structures is a distinct feature of necrosis (Figures S6B–S6D). This was confirmed by immunogold EM (Figure 6F). When HeLa cells, which do not express endogenous RIP3, were transfected with RIP3-mCherry and stimulated with TNF, zVAD-fmk, and LBW242 to induce necrosis, they showed complete overlap of ThT staining with RIP3-mCherry puncta (Figure 6G).
As expected, WT RIP3-transfected cells underwent cell death, whereas the RHIM AAAA mutant was highly protected. Importantly, RIP3 mutants V458P, V460P, and G457D protected cells from TNF-induced necrosis, whereas the mutant N464D that did not show significant defects in vitro behaved most similar to the WT (Figure 7A). In addition, mutants V458P and V460P completely abolished puncta formation in response to necrosis stimulation, whereas G457D partially disrupted RIP3 clustering (Figure 7B).
Protein: DP04295 (UniProt Q9Y572)
Region: residues 457	to 461
Annotation: necroptotic process (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
RHIM Residues of RIP1 and RIP3 Are Crucial for Cluster Formation, Kinase Activation, and Programmed Necrosis
For RIP3, we stimulated HeLa cells transfected with WT and mutant RIP3-yellow fluorescent protein (YFP) with TNF, zVAD-fmk, and LBW242. As expected, WT RIP3-transfected cells underwent cell death, whereas the RHIM AAAA mutant was highly protected. Importantly, RIP3 mutants V458P, V460P, and G457D protected cells from TNF-induced necrosis, whereas the mutant N464D that did not show significant defects in vitro behaved most similar to the WT (Figure 7A).
Protein: DP04295 (UniProt Q9Y572)
Region: residues 457	to 461
Annotation: activation of protein kinase activity (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
RHIM Residues of RIP1 and RIP3 Are Crucial for Cluster Formation, Kinase Activation, and Programmed Necrosis
Expression of RIP3-YFP in 293T cells showed that the mutations V458P and V460P severely compromised RIP3 kinase activation by using myelin basic protein (MBP) as the substrate (Figure S7A). To further validate the results from transient expression, we stably reconstituted RIP3−/− fibroblasts with WT and mutant RIP3. In agreement with results in 293T cells, WT RIP3 showed robust kinase activity upon induction of necrosis, whereas the V458P, V460P, and G457D mutants were dramatically impaired in kinase activation (Figure 7C).
Protein: DP04295 (UniProt Q9Y572)
Region: residues 300	to 518
Annotation: disorder (Structural state)
Evidence: author inference based on intrinsic disorder prediction used in manual assertion
Supporting statements:
We investigated why RIP1/3-RHIM and RIP1/3-FL could form such large complexes. Secondary structure predictions suggested that the region between the KD and the DD in RIP1 (~residues 300–560) and the region C-terminal to the KD in RIP3 (~residues 300-end) are mostly unstructured random coils (Rost et al., 2004).
Protein: DP04296 (UniProt Q12517)
Region: residues 1	to 16
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several regions of the polypeptide are not visible in the electron density map and are assumed to be disordered, namely residues 1-21, 74-134 and 229-231 for molecule A, and residues 1-16 and 81-134 for molecule B in the crystallographic asymmetric unit. 
Cross-references: PDB:1Q67
Protein: DP04296 (UniProt Q12517)
Region: residues 81	to 134
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several regions of the polypeptide are not visible in the electron density map and are assumed to be disordered, namely residues 1-21, 74-134 and 229-231 for molecule A, and residues 1-16 and 81-134 for molecule B in the crystallographic asymmetric unit. 
Cross-references: PDB:1Q67
Protein: DP04297 (UniProt Q9NPJ4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–130 of Dcp1aEVH1 and a stretch of PNRC2 polypeptide chain comprising 14 residues (residues 102 to 115) are visible in the electron density map with the rest of the residues in PNRC2 (residues 1–101 and residues 116–121) assumed to be disordered as there is no interpretable electron density for these regions. 
Cross-references: PDB:4B6H