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PMC:7553147 / 32151-36194 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T63 1049-1053 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T64 1193-1198 Body_part denotes thumb http://purl.org/sig/ont/fma/fma24938
T65 1731-1735 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T66 1779-1790 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T67 1887-1898 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T68 3290-3298 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T69 3346-3350 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T70 3427-3434 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T10 1193-1198 Body_part denotes thumb http://purl.obolibrary.org/obo/UBERON_0001463
T11 3346-3350 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T43 1088-1091 Disease denotes PC1 http://purl.obolibrary.org/obo/MONDO_0008173
T44 1177-1180 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T46 1358-1361 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T48 1453-1456 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T50 2138-2141 Disease denotes PC3 http://purl.obolibrary.org/obo/MONDO_0014324
T51 3307-3310 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T53 3556-3564 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T218 43-44 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T219 129-130 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T220 378-381 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T221 394-395 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T222 438-439 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T223 503-504 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T224 545-546 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T225 644-645 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T226 675-676 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T227 737-738 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T228 780-781 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T229 858-859 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T230 927-928 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T231 1029-1036 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T232 1125-1132 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T233 1151-1152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T234 1185-1188 http://purl.obolibrary.org/obo/CLO_0008975 denotes SD1
T235 1307-1309 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T236 1368-1369 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T237 1494-1495 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T238 1512-1513 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T239 1555-1556 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T240 1936-1937 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T241 2138-2141 http://purl.obolibrary.org/obo/CLO_0008395 denotes PC3
T242 2138-2141 http://purl.obolibrary.org/obo/CLO_0051535 denotes PC3
T243 2138-2141 http://purl.obolibrary.org/obo/CLO_0052068 denotes PC3
T244 2138-2141 http://purl.obolibrary.org/obo/CLO_0052069 denotes PC3
T245 2138-2141 http://purl.obolibrary.org/obo/CLO_0052070 denotes PC3
T246 2138-2141 http://purl.obolibrary.org/obo/CLO_0052071 denotes PC3
T247 2145-2146 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T248 2173-2174 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T249 2585-2586 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T250 2622-2623 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T251 2686-2687 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T252 2872-2873 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 2916-2917 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 3272-3273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T255 3370-3371 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T256 3708-3709 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T257 3749-3750 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T258 3785-3786 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T259 3824-3825 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T260 3839-3842 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T8 3259-3268 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T222 0-2 Sentence denotes 4.
T223 4-17 Sentence denotes Conclusions  
T224 18-281 Sentence denotes In this work, we present a clear example of how the structural discovery process can be greatly accelerated by a wise combination of rapid data sharing and the use of the wave of newly developed algorithms that characterize this phase of the ‘cryo-EM revolution’.
T225 282-473 Sentence denotes The reanalysis of the data used in Wrapp et al. (2020 ▸), but with new workflows and new tools, has resulted in a rich analysis of the spike flexibility as a key characteristic of the system.
T226 474-647 Sentence denotes Essentially, and at least to a first approximation, the spike moves in a continuous manner with no preferential states, as clearly shown in the scatter plots in Fig. 3 ▸(b).
T227 648-825 Sentence denotes In this way, the result of a particular instance of image-processing analysis, including a 3D classification, should be regarded as a snapshot of this quasi-continuum of states.
T228 826-1078 Sentence denotes In our case, we have shown that a particular meta image-classification approach, implemented through a consensus among different methods in many steps of the analysis, results in classes that are at the extreme of the main axis of variance in PC space.
T229 1079-1311 Sentence denotes Clearly, PC1, through the analysis of the two extreme classes, reflects a concerted motion of the NTD–RBD–SD1–SD2 thumb, although there are smaller collective movements throughout the spike (see Fig. 2 ▸ and Supplementary Movie S1).
T230 1312-1448 Sentence denotes In this case, the RBD moves together with the NTD, with a smaller degree of independent flexibility and always in the ‘up’ conformation.
T231 1449-1702 Sentence denotes The NTD–RBD movement can be characterized to a large degree as a rotation, but the different RBDs present a much more complex pattern of flexibility, indicating an important structural rearrangement [from elastic analysis (Fig. 2 ▸) and PCA (Fig. 3 ▸)].
T232 1703-1979 Sentence denotes The presence of quasi-solid body rotation hinges is clearly located between amino acids 318–326 and 588–595, which produce most of the displacement, together with other hinges between amino acids 330–335 and 527–531, which accompany a less pronounced ‘up’ movement of the RBD.
T233 1980-2137 Sentence denotes However, there are other PC axes explaining significant fractions of the inter-image variance that are not properly explored at the level of our two classes.
T234 2138-2328 Sentence denotes PC3 is a clear example, indicating a high variance at the voxels associated with RBD up, which probably suggests large conformational changes in this area that result in the RBD moving down.
T235 2329-2682 Sentence denotes The flexibility analysis performed in this work complements previous analysis showing large rotations together with RBD up–down structural changes (Pinto et al., 2020 ▸; Wrapp et al., 2020 ▸), in the sense that the different studies present ‘snapshots’ of a continuum of movements obtained by a particular instance of an image-processing classification.
T236 2683-2812 Sentence denotes In a sense, all of these results are correct, but none of them is able to capture the richness of the flexibility of this system.
T237 2813-3050 Sentence denotes This fact reflects the intrinsic instability of segmenting a continuum into defined clusters, which is a clear limitation of the classification approaches that needs to be considered in detailed analysis of any data set from this system.
T238 3051-3332 Sentence denotes An obvious way to increase the resolution of the moving parts of the spike is to reduce their mobility, as is the case, for instance, in the biochemical stabilization of Hsieh et al. (2020 ▸) and also in the formation of a complex with an antibody against NTD (Chi et al., 2020 ▸).
T239 3333-3702 Sentence denotes On the other hand, the route towards a more complete analysis of the flexibility of the spike protein necessarily involves the analysis of data sets that are quite substantially larger than those being used in most current SARS-CoV-2 studies, so that all of the main axes of inter-image variability can be explored; this is work that is under development at the moment.
T240 3703-4043 Sentence denotes From a biomedical perspective, the proof that a quasi-continuum of flexibility is a key characteristic of this specimen, a concept that has been implicitly considered in much of the structural work performed so far but never demonstrated, suggests that ways to interfere with this flexibility could be important components of new therapies.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
191 417-422 Gene denotes spike Gene:43740568
197 1263-1268 Gene denotes spike Gene:43740568
198 1185-1188 Gene denotes SD1 Gene:57306
199 530-535 Gene denotes spike Gene:43740568
200 1719-1751 Disease denotes quasi-solid body rotation hinges MESH:D009069
201 1088-1091 CellLine denotes PC1 CVCL:0152
203 2138-2141 Gene denotes PC3 Gene:57332
205 2477-2482 Gene denotes Pinto Gene:668
210 3120-3125 Gene denotes spike Gene:43740568
211 3421-3426 Gene denotes spike Gene:43740568
212 3556-3566 Species denotes SARS-CoV-2 Tax:2697049
213 3221-3226 Disease denotes Hsieh