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PMC:7605337 / 19990-23860 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T49 1554-1562 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T50 2640-2650 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T115 297-301 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T116 307-316 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T117 370-374 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T118 379-388 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T119 404-408 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T120 468-477 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T121 543-547 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T122 657-661 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T123 769-778 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T124 783-787 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T125 802-811 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T126 846-855 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T127 890-899 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T128 1911-1920 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T129 2019-2023 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T130 2750-2759 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T131 2761-2765 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T132 2819-2828 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T133 2865-2869 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T134 2881-2890 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T135 2985-2989 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T136 3029-3038 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T137 3043-3047 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T138 3138-3142 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T139 3556-3565 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T140 3570-3574 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T141 3747-3751 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T142 3825-3834 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T123 413-416 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T124 417-418 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T125 508-509 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 529-530 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T127 581-582 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T128 632-633 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T129 724-725 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 796-797 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 1055-1056 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 1153-1154 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T133 1169-1170 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T134 1249-1250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 1272-1273 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T136 1361-1362 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 1384-1385 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T138 1428-1429 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 1450-1451 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T140 1525-1528 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2 Å
T141 1684-1686 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T142 1885-1887 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T143 1885-1887 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T144 1977-1978 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T145 2058-2059 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T146 2187-2188 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 2216-2217 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T148 2234-2235 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T149 2314-2315 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 2348-2349 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T151 2366-2367 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T152 2427-2428 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T153 2955-2958 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T154 2977-2978 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T155 3060-3063 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T156 3097-3098 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T157 3272-3273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 3286-3287 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T159 3311-3312 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T160 3329-3330 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T161 3357-3360 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T162 3361-3362 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T163 3386-3387 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T164 3436-3437 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 3468-3469 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T76 132-137 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T77 225-230 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T78 1856-1861 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T79 1885-1887 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T80 2640-2650 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T81 2640-2645 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T82 2646-2650 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T83 3527-3529 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T6 71-84 http://purl.obolibrary.org/obo/GO_0006412 denotes translational
T7 877-886 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviors
T8 1347-1355 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior
T9 2622-2630 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T103 0-19 Sentence denotes Structural Dynamics
T104 20-253 Sentence denotes To compute the RMSD of systems, the rotational and translational movements were removed by first fitting the Cα atoms of the RBD to the crystal structure and then computing the RMSD with respect to the Cα atoms of RBD in each system.
T105 254-343 Sentence denotes Figure 3 shows the RMSD plot in the RBD of SARS-COV, nCOV-2019, and some of its variants.
T106 344-464 Sentence denotes Comparison of the RMSD of SARS and nCOV-2019 RBD shows that SARS-COV has a larger RMSD throughout the 500 ns simulation.
T107 465-634 Sentence denotes In nCOV-2019, the RMSD is very stable with a value of about 1.5 Å, whereas in SARS-COV, the RMSD increases up to ∼4 Å after 100 ns and then fluctuates between 3 and 4 Å.
T108 635-740 Sentence denotes The change in RMSD of SARS is partially related to the motion in the C-terminal which is a flexible loop.
T109 741-822 Sentence denotes Figure 3 Cα RMSD plots for nCOV-2019 and SARS-COV and a few nCOV-2019 mutations.
T110 823-903 Sentence denotes The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt.
T111 904-1045 Sentence denotes In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations.
T112 1046-1097 Sentence denotes However, a few mutations showed some RMSD variance.
T113 1098-1185 Sentence denotes In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns.
T114 1186-1298 Sentence denotes Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward.
T115 1299-1386 Sentence denotes The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å.
T116 1387-1452 Sentence denotes Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å.
T117 1453-1529 Sentence denotes For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å.
T118 1530-1632 Sentence denotes These variations in the backbone RMSD show the involvement of these residues in the complex stability.
T119 1633-1687 Sentence denotes RMSD plots for other mutations are shown in Figure S1.
T120 1688-1889 Sentence denotes Since the extended loop (residues 449 to 510 shown in Figure 1B from α4 to α5) of the RBD makes all contacts with ACE2, the RMSD was computed by also fitting to the Cα atoms of this region (Figure S2).
T121 1890-2060 Sentence denotes The extended loop in nCOV-2019 is very stable with less deviation (RMSD = 0.86 ± 0.017 Å) from the crystal structure compared to SARS-COV having an RMSD of 2.79 ± 0.05 Å.
T122 2061-2136 Sentence denotes Few of the mutants show an increase in the loop RMSD during the simulation.
T123 2137-2284 Sentence denotes In mutants N487A and Y449A the loop RMSD jumps to a value of about 1.95 ± 0.12 Å and 1.94 ± 0.24 Å, respectively, after about 200 ns of simulation.
T124 2285-2405 Sentence denotes Mutants G447A and E484A show a loop RMSD values of 2.22 ± 0.03 Å and 1.96 ± 0.02 Å during the last 100 ns of simulation.
T125 2406-2492 Sentence denotes Other mutants showed a stable extended loop (observed in loop RMSD) during simulation.
T126 2493-2593 Sentence denotes The stability of extended loop for mutant systems confirms the high tolerance of this region of RBD.
T127 2594-2730 Sentence denotes To characterize the dynamic behavior for each amino acid in the RBD, we analyzed the root mean square fluctuation (RMSF) of all systems.
T128 2731-2874 Sentence denotes The RMSF plots for nCOV-2019, SARS-COV, and four other mutations are shown in Figure 4. nCOV-2019 shows less fluctuations compared to SARS-COV.
T129 2875-3017 Sentence denotes L3 in nCOV-2019 corresponding to residues 476 to 487 (shown in red in Figure 4) has smaller RMSF (1.5 Å) than SARS-COV L3 residues 463 to 474.
T130 3018-3100 Sentence denotes L1 in both nCOV-2019 and SARS-COV (green) has small fluctuation (less than 1.5 Å).
T131 3101-3196 Sentence denotes Moreover, the C-terminal residues of SARS-COV show high fluctuation (Figure 4 shown in orange).
T132 3197-3243 Sentence denotes Few mutants show higher fluctuation in the L1.
T133 3244-3341 Sentence denotes Mutants Y505A and S494A had a RMSF of 2.5 Å and mutation N487A had a RMSF of about 4 Å in the L1.
T134 3342-3398 Sentence denotes Mutation Y449A has a higher RMSF of about 3 Å in the L3.
T135 3399-3480 Sentence denotes Mutants G496A, E484A, and G447A show a high fluctuation of about 4.5 Å in the L3.
T136 3481-3530 Sentence denotes The RMSF of other variants is shown in Figure S3.
T137 3531-3611 Sentence denotes Figure 4 RMSF plots for nCOV-2019-wt, SARS-COV, Y505A, N487A, G496A, and E484A.
T138 3612-3718 Sentence denotes The red shaded region shows the fluctuation in L1 and the green shaded region shows the fluctuation in L3.
T139 3719-3796 Sentence denotes The orange shaded region in SARS-COV shows the fluctuation in the C-terminal.
T140 3797-3870 Sentence denotes For comparison, the RMSF of nCOV-2019-wt is shown as cyan in other plots.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
452 297-305 Species denotes SARS-COV Tax:694009
453 307-311 Species denotes nCOV Tax:2697049
454 379-383 Species denotes nCOV Tax:2697049
455 404-412 Species denotes SARS-COV Tax:694009
456 468-472 Species denotes nCOV Tax:2697049
457 543-551 Species denotes SARS-COV Tax:694009
461 769-773 Species denotes nCOV Tax:2697049
462 783-791 Species denotes SARS-COV Tax:694009
463 802-806 Species denotes nCOV Tax:2697049
466 846-850 Species denotes nCOV Tax:2697049
467 890-894 Species denotes nCOV Tax:2697049
473 1802-1806 Gene denotes ACE2 Gene:59272
474 1763-1765 Gene denotes α5 Gene:28884
475 1757-1759 Gene denotes α4 Gene:28898
476 1911-1915 Species denotes nCOV Tax:2697049
477 2019-2027 Species denotes SARS-COV Tax:694009
487 2750-2754 Species denotes nCOV Tax:2697049
488 2761-2769 Species denotes SARS-COV Tax:694009
489 2819-2823 Species denotes nCOV Tax:2697049
490 2865-2873 Species denotes SARS-COV Tax:694009
491 2881-2885 Species denotes nCOV Tax:2697049
492 2985-2993 Species denotes SARS-COV Tax:694009
493 3029-3033 Species denotes nCOV Tax:2697049
494 3043-3051 Species denotes SARS-COV Tax:694009
495 3138-3146 Species denotes SARS-COV Tax:694009
500 3556-3560 Species denotes nCOV Tax:2697049
501 3570-3578 Species denotes SARS-COV Tax:694009
502 3747-3755 Species denotes SARS-COV Tax:694009
503 3825-3829 Species denotes nCOV Tax:2697049