LiteFold/DisProt huggingface dataset:
Protein: DP00842 (UniProt P12506)
Region: residues 1	to 86
Annotation: viral gene expression (Biological process)
Evidence: beta-galactosidase reporter gene assay evidence used in manual assertion
Supporting statements:
In each case, Tat was added to the cell buffer, and therefore expression of β-gal up to the control means that the synthetic Tat was able to cross the cytoplasmic and nucleus membranes, bind TAR, and interact with cellular cofactors.
The authors show an increase in β-galactosidase expression through a transactivation assay with HeLa cells transfected with a LTR HIV-1 β-gal plasmid and purified TAT protein.
Protein: DP00845 (UniProt P23632)
Region: residues 95	to 107
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
All peptides showed very poor NOESY spectra at 20°C (1-3).
Peptide R13 did not show any long-range NOE (more than four residues apart) and only two medium-range NOEs, suggesting that this peptide behaves as a random coil in solution, not showing any structural tendency.
Protein: DP00847 (UniProt P20220)
Region: residues 74	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interpretable electron density begins at the N-terminus with residue 4 of the native sequence and ends at residue 73. Residues 74 through 112 were not visible in the electron density, and accordingly not modelled.
Cross-references: PDB:2VQC
Protein: DP00849 (UniProt Q9Q8E9)
Region: residues 1	to 32
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure contains 32 unstructured residues at the N terminus, one α-helix (residues 74–79) and five β-strands (residues 35–42, 47–50, 58–61, 83–91, and 95–99). The antiparallel β-strands are arranged in the order 3–2–1–4–5, with the first four strands in the Greek key topology.
Cross-references: PDB:1JJG
Protein: DP00849 (UniProt Q9Q8E9)
Region: residues 62	to 73
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues 62–73 of the loop preceding the α-helix had few structural restraints and this sequence therefore has a large variability in structural coordinates among the ensemble of structures.
Cross-references: PDB:1JJG
Protein: DP00849 (UniProt Q9Q8E9)
Region: residues 62	to 73
Annotation: phosphorylation display site (Disorder function)
Evidence: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
Supporting statements:
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of in vitro phosphorylated M156R revealed that approximately 75% of the phosphorylation occurred in the peptide LLGYEGHECILLDYLNYR, which includes Y67. Fragmentation analysis indicated that Y54, Y64 or Y67 could be phosphorylated (data not shown).
Cross-references: PDB:1JJG
Protein: DP00850 (UniProt P36932)
Region: residues 46	to 161
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The P2 Int45–337 construct used yielded crystals from which X-ray diffraction data to 1.9 Å was collected (see Table 1). However, the collected data only revealed electron density corresponding to the C-terminal catalytic domain of P2 Int.
The N-terminal arm-binding domain of λ is disordered in the crystal structure.
Cross-references: PDB:5C6K
Protein: DP00861 (UniProt Q9L9I0)
Region: residues 123	to 151
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
ZraP is revealed as a decameric structure within which the  ZraP  monomer  is  composed  of  two α-helices  and  residues 123–151  are  disordered  (Figures  3A  and  3B).
Cross-references: PDB:3LAY
Protein: DP00861 (UniProt Q9L9I0)
Region: residues 1	to 42
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure, indicating it is disordered.
Protein: DP00866 (UniProt O54465)
Region: residues 42	to 72
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although secondary structure prediction indicates an additional C-terminal α-helical region between residues 40 and 72 (Fig. 3a), this sequence is flexible and does not adopt a unique structure in solution.
Cross-references: PDB:2L8T
BMRB:17425
Protein: DP00866 (UniProt O54465)
Region: residues 42	to 72
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The N-terminal arms were disordered in 80α virions, but are ordered in both SaPI1 and 80α procapsids, suggesting that both gp6 and gp47 become ordered upon binding 21.
Cross-references: EMDB:1869
Protein: DP00870 (UniProt H0W0T5)
Region: residues 364	to 565
Annotation: limited proteolysis display site (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Although our results are consistent with the first cleavage site (residue 364), it is also possible that the residues were disordered up to the second cleavage site (residue 372), and no electron density was observed (34).
Apparently proteolysis occurring during the 2 weeks required for crystal growth released the catalytic domain, and it is only this that could form well ordered crystals. 
Cross-references: PDB:4R8K
PDB:4R8L
Protein: DP00871 (UniProt A4ZNR2)
Region: residues 1	to 121
Annotation: molten globule (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Interestingly, the near-UV CD spectrum obtained at near physiological buffer conditions was virtually zero, and resembled the spectrum of the protein in the presence of 6m GdmCl (Fig. 3). These observations suggest that under native buffer conditions, the aromatic groups of NS2 are able to rotate freely and undergo no strong interactions with other groups within NS2 (48).
While far-UV CD and FT-IR spectroscopy detected the presence of a significant amount of secondary structure in NS2, near-UV CD and fluorescence spectroscopy revealed that the aromatic residues of the protein were highly assessable to the solvent, and did not undergo strong interactions with neighboring groups.
The flexibility observed in NS2 was intriguing, as with a length of 121 residues the protein is by far large enough to fold independently. The unusual set of characteristics found in the structure of NS2 (compactness, presence of a pronounced secondary structure, but absence of a tightly packed tertiary structure) are attributes typically connected with the molten globule state of proteins (52, 60).
Protein: DP00871 (UniProt A4ZNR2)
Region: residues 1	to 121
Annotation: molten globule (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
As expected, these results indicate that the unfolding of NS2 is dominated by the unfolding of its secondary structure. Assuming a two-state mechanism of unfolding, the conformational stability ΔG(H20) of NS2 was estimated as about 6 kcal/mol as described in Ref. 38 (TableII). This value is at the lower end of the range of stabilities commonly observed for solvent-induced unfolding of globular proteins (ΔG(H20) ≈ 5–10 kcal/mol) (55).
The flexibility observed in NS2 was intriguing, as with a length of 121 residues the protein is by far large enough to fold independently. The unusual set of characteristics found in the structure of NS2 (compactness, presence of a pronounced secondary structure, but absence of a tightly packed tertiary structure) are attributes typically connected with the molten globule state of proteins (52, 60).
Protein: DP00871 (UniProt A4ZNR2)
Region: residues 1	to 121
Annotation: molten globule (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
In contrast, if NS2 was added to ANS in the presence of 6 m GdmCl, no such interaction was observed. These results suggest that NS2 possesses a loosely packed hydrophobic core that is accessible to the solvent, as expected for a folded protein with a dynamic tertiary structure.
Furthermore, isolated NS2 strongly interacted with the hydrophobic dye ANS suggesting that hydrophobic clusters within the structure of the protein were assessable to the solvent as well (51).
Addition of acrylamide led to rapid quenching of the tryptophan fluorescence, comparable to tryptophan quenching under denaturing conditions (TableI). The Stern-Volmer plot of the quenching reaction showed upward curvature, indicating that both tryptophan residues of NS2 were nearly equally assessable to the solvent (Fig. 4) (34).
While far-UV CD and FT-IR spectroscopy detected the presence of a significant amount of secondary structure in NS2, near-UV CD and fluorescence spectroscopy revealed that the aromatic residues of the protein were highly assessable to the solvent, and did not undergo strong interactions with neighboring groups.
The flexibility observed in NS2 was intriguing, as with a length of 121 residues the protein is by far large enough to fold independently. The unusual set of characteristics found in the structure of NS2 (compactness, presence of a pronounced secondary structure, but absence of a tightly packed tertiary structure) are attributes typically connected with the molten globule state of proteins (52, 60).
There are two expermiments done with different fluorescence evidence: intrinsic florescence (tryptophan) and dye fluorescence (ANS).
Protein: DP00871 (UniProt A4ZNR2)
Region: residues 1	to 121
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
These observations altogether indicate specific molecular association between M1 and NS2.
Since the NS2 protein was not detected in the M1-free RNP peak (Figs. 3B and 3C; fractions 3-5), we concluded that NS2 is able to rebind RNP cores in vitro only in the simultaneous presence of M1.
The above observation suggested direct physical association between M1 and NS2.
Protein: DP00871 (UniProt A4ZNR2)
Region: residues 1	to 121
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
A functional domain on the NS2 with characteristics of a nuclear export signal was mapped: it interacts with cellular nucleoporins, can functionally replace the effector domain of the human immunodeficiency virus type 1 (HIV-1) Rev protein and mediates rapid nuclear export when cross-linked to a reporter protein.
In the yeast two-hybrid system, only the viral NS2 protein was able to interact with different nucleoporins.
The NEP of influenza virus was able to interact strongly with Rab/hRIP1 and yRip1, less strongly with yNup100 and yNup116, and not with yNup1.
Protein: DP00871 (UniProt A4ZNR2)
Region: residues 11	to 23
Annotation: protein export from nucleus (Biological process)
Evidence: immunolocalization evidence used in manual assertion
Supporting statements:
A functional domain on the NS2 with characteristics of a nuclear export signal was mapped: it interacts with cellular nucleoporins, can functionally replace the effector domain of the human immunodeficiency virus type 1 (HIV-1) Rev protein and mediates rapid nuclear export when cross-linked to a reporter protein.
GST-x-NEP quickly migrated to the cytoplasm after microinjection into the nuclei of Madin–Darby bovine kidney (MDBK) cells (Figure 4A and C).
Therefore, we conclude that the NEP protein contains an NES within amino acids 11– 23.
Protein: DP00875 (UniProt P69723)
Region: residues 141	to 192
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of the CTD (Fig. 2A) lacked the typical signatures of secondary structure, exhibiting only a negative signal at 200 nm. This pattern implied a high content of unstructured regions in the CTD.
To avoid on-resin aggregation during the synthesis authors substituted the residues 185, 179, 169 and 143 with pseudoproline dipeptide.
Protein: DP00875 (UniProt P69723)
Region: residues 141	to 192
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the CTD (Fig. 5A) in 5.4 mM DPC (green) and in 20 mM DPC (red), compared with the spectrum in buffer without DPC (blue), showed a red shift of ∼3 nm (from 199 to 202 nm). The minimum at 198 nm decreased, while the signal at 222 nm increased. The change in the CD spectrum indicates a structural change in the Vif CTD that was induced by the micellar environment.
Protein: DP00875 (UniProt P69723)
Region: residues 141	to 192
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The CTD eluted from the column with an elution volume of 11.3 ml. This volume gave an apparent molecular weight of 14.0 kDa, a value 2.5 times higher than the calculated mass of 5.8 kDa according to the calibration curve of standard MW markers. This indicated an extended conformation of the Vif CTD.
Protein: DP00875 (UniProt P69723)
Region: residues 145	to 192
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-NMR spectra of Vif145–192 showed a narrow dispersion of amide resonances, which is characteristic of a random coil (Fig. 4A). 
The dispersion of the amide protons in the 15N-HSQC spectrum (Fig. 4B) was in a narrow range of 7.95–8.74 ppm, Δ = 0.79 ppm, characteristic of unfolded proteins and peptides.
Protein: DP00875 (UniProt P69723)
Region: residues 141	to 192
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the CTD (Fig. 5A) in 5.4 mM DPC (green) and in 20 mM DPC (red), compared with the spectrum in buffer without DPC (blue), showed a red shift of ∼3 nm (from 199 to 202 nm). The minimum at 198 nm decreased, while the signal at 222 nm increased. The change in the CD spectrum indicates a structural change in the Vif CTD that was induced by the micellar environment.
Protein: DP00875 (UniProt P69723)
Region: residues 141	to 192
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Vif141–192 was titrated into fluorescein-labeled ElonginC76–111 and the resulting binding curve was fit to 1:1 binding model, resulting in Kd of 11.0 ± 0.6 µM (Fig. 5B).
Protein: DP00875 (UniProt P69723)
Region: residues 145	to 192
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Vif145–192 bound the ElonginC peptide with similar affinity, Kd = 12.5 ± 0.3 µM.
Protein: DP00875 (UniProt P69723)
Region: residues 141	to 192
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of Vif CTD—ElonginC76–111 mixture at 1:1 molar ratio (Fig. 5C) gave an average between the unbound spectra of the CTD and the free ElonginC76–111, indicating that there is no significant change in the CTD structure upon binding to ElonginC76–111 at this molar ratio.
Protein: DP00875 (UniProt P69723)
Region: residues 157	to 192
Annotation: viral genome replication (Biological process)
Evidence: cell transfection experiment evidence used in manual assertion
Supporting statements:
Membrane localization is required for Vif function during HIV-1 replication. To provide a quantitative measure of the biological activity of the mutant Vif proteins, a transient complementation assay was used to examine the abilities of the mutant Vif proteins to complement a single round of HIV-1 replication in trans (Fig. 3) (5, 13). The expression of wild-type Vif in trans in this assay restores the replication of a  vif-defective virus to the wild-type level (5, 8). In the absence of Vif expressed in trans, replication of the vif-positive virus was approximately 10-fold greater than that of the vif-negative virus.
Protein: DP00875 (UniProt P69723)
Region: residues 157	to 192
Annotation: plasma membrane (Cellular component)
Evidence: cell transfection experiment evidence used in manual assertion
Supporting statements:
The biological activities of the mutant Vif proteins correlated directly with their membrane binding activities in vitro (Fig. 3), indicating that Vif function is likely to require membrane localization.
However, no virus replication was detected in H9 cultures transfected with the B1,  B2, or B4 HIV-1 mutant virus DNAs. These results confirm the absence or near absence of Vif function in the B1, B2, and B4 mutants during HIV-1 replication in nonpermissive cells. Moreover, the direct correlation between the loss of biological activity and the loss of membrane binding of Vif during HIV-1 replication in infected cells (Fig. 2B) indicates that membrane localization is likely to be required for Vif function in vivo.
Virus replication was monitored by measuring the reverse transcriptase activity in the culture supernatant.
Protein: DP00875 (UniProt P69723)
Region: residues 157	to 192
Annotation: viral genome replication (Biological process)
Evidence: southern hybridization evidence used in manual assertion
Supporting statements:
Full-genome-length minus-strand DNA was not detectable in vif mutant virions even when the blots were overexposed to visualize the short DNA products at an intensity similar to that of the wild type. The blots were rehybridized with the gag/pol(2) probe, which detects minus-strand DNA which has been reverse transcribed through the left half of the genome. Hybridization with the gag/pol(2) probe gave results similar to those obtained with the U3(2) probe, indicating that minus-strand synthesis was discontinuous with initiation at multiple sites.
The preceding experiment indicates that vif mutant virions are defective in their ability to synthesize minus-strand DNA. To determine the effect of Vif on synthesis of the plus strand, the blots from the preceding experiment were reprobed with U3 and gag/pol riboprobes of minus-strand polarity. The U3(1) probe detects initial plus-strand DNA products immediately adjacent to the 39 PPT. The gag/pol(1) probe detects plus-strand DNA products synthesized after the second template switch or initiated at the central PPT. In wild-type virions, the U3(1) and gag/pol(1) probes detected plus-strand DNA products of 0.5 to 9.7 kb (Fig. 3B). In contrast, plus-strand DNA products longer than 4 kb could not be detected in vif mutant virions even when the blots were overexposed to visualize the short DNA products at an intensity similar to that of the wild type.
Protein: DP00876 (UniProt P14340)
Region: residues 676	to 775
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows the disorder region from 676-775 (envelope protein E).
Cross-references: PDB:4UIH
Protein: DP00876 (UniProt P14340)
Region: residues 2742	to 2761
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows the disorder region from 2742-2761 (NS5 RNA-dependent RNA polymerase).
Cross-references: PDB:6IZX
PDB:6IZY
Protein: DP00876 (UniProt P14340)
Region: residues 2947	to 2963
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows the disorder region from 2947-2963 (NS5 RNA-dependent RNA polymerase).
Cross-references: PDB:6IZX
PDB:6IZY
Protein: DP00876 (UniProt P14340)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The main structural regions are distinguished by their average backbone solvent accessibility (Fig. 3, left panel): the disordered N-terminal backbone is highly exposed, the flexible fold is partially accessible, and the conserved fold is mostly inaccessible to the solvent.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
We found that Pup runs at 14 kDa on an SDS gel as demonstrated previously.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Moreover, a CD spectrum of Pup under physiological condition displays a single minimum, at approx. 200 nm,
which is the characteristic of unstructured proteins (Figure 2D).
This observation further strengthens the suggestion that Pup is an
IDP. Meanwhile, there is a broad but weak negative ‘shoulder’
peak between 218 nm and 230 nm, implying the existence of
a small proportion of residual secondary structure
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Puriﬁed Pup displays an apparent molecular mass of 18 kDa
(Figure 2C), in comparison to a theoretical molecular mass of
8 kDa. The abnormal electrophoresis shift rate of Pup in SDS/PAGE might reﬂect its amino acid composition bias and extended
conformation.
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A spectrum recorded on Pup reflects that
of a disordered polypeptide with negative ellipticity near 200 nm and low ellipticity at 190 and
222 nm (Figure 3a). Moreover, induced thermal melting did not produce the spectral transition
characteristic of cooperative protein unfolding, thus providing further evidence for Pup being
an intrinsically disordered protein (Figure 3b).
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Size exclusion chromatrography by FPLC reveals that 6.9 kDa Pup has a larger
hydrodynamic radius than 8.6 kDa ubiquitin.
Pup also elutes earlier than expected during size exclusion
chromatography however. It directly follows the 16.7 kDa ubiquitin receptor Rpn13 and elutes
significantly earlier than 8.6 kDa ubiquitin (Figure 1b), which forms a compact structure
(Figure 1c)
Protein: DP00877 (UniProt P9WHN5)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Even in the absence of denaturant, the CD spec-
trum of Pup displays a strongly negative mean molar ellipticity
with a minimum at slightly below 200 nm, a feature indicative of
poorly structured proteins. However, a broad and low-amplitude negative band at around 225 nm predicts a low content of second-
ary structure.
CD analysis of Pup indicates that Pup is mostly disordered and
contains only a small amount of secondary structure.