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PMC:7441777 / 23528-28835 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T38 399-407 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T39 1156-1167 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T40 1187-1193 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T41 1431-1439 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T42 1605-1613 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T43 1620-1626 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T44 1815-1817 Body_part denotes Å2 http://purl.org/sig/ont/fma/fma66595
T45 4144-4150 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T46 4196-4203 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T47 4992-4999 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T48 5084-5086 Body_part denotes Å2 http://purl.org/sig/ont/fma/fma66595
T49 5149-5153 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T50 5209-5211 Body_part denotes Å2 http://purl.org/sig/ont/fma/fma66595
T51 5289-5296 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 5149-5153 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T70 222-230 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T141 150-153 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T142 520-521 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T143 552-553 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T144 742-743 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T145 750-751 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T146 758-759 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T147 766-767 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T148 774-775 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T149 782-783 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T150 790-791 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T151 798-799 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T152 809-810 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T153 937-940 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T154 1185-1186 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T155 1199-1200 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T156 1371-1372 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T157 1451-1452 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T158 1796-1797 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T159 1805-1806 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T160 1815-1817 http://purl.obolibrary.org/obo/CLO_0001562 denotes Å2
T161 1815-1817 http://purl.obolibrary.org/obo/CLO_0001563 denotes Å2
T162 2291-2294 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T163 2638-2641 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T164 2657-2658 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 2722-2723 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T166 2875-2876 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T167 3039-3040 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T168 3074-3075 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T169 3224-3225 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T170 3286-3287 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 3363-3369 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T172 4362-4363 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T173 4371-4372 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T174 4380-4381 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T175 4389-4390 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T176 4398-4399 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T177 4407-4408 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T178 4416-4417 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T179 4425-4426 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T180 4437-4438 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T181 4539-4542 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T182 5017-5018 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 5084-5086 http://purl.obolibrary.org/obo/CLO_0001562 denotes Å2
T184 5084-5086 http://purl.obolibrary.org/obo/CLO_0001563 denotes Å2
T185 5209-5211 http://purl.obolibrary.org/obo/CLO_0001562 denotes Å2
T186 5209-5211 http://purl.obolibrary.org/obo/CLO_0001563 denotes Å2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T337 132-142 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T338 144-148 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T339 167-170 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T340 172-182 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T341 184-193 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T343 199-212 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T344 408-413 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T345 820-830 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T346 837-841 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T347 848-851 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T348 880-889 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T350 896-909 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T351 916-926 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T352 1035-1044 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T354 1156-1167 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T355 1156-1161 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T356 1162-1167 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T357 1210-1219 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T358 1440-1445 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T359 1502-1507 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T360 1650-1657 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T361 1885-1889 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T362 1940-1943 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T363 2105-2114 Chemical denotes Myricetin http://purl.obolibrary.org/obo/CHEBI_18152
T364 2166-2179 Chemical denotes Quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T365 2230-2240 Chemical denotes Hesperidin http://purl.obolibrary.org/obo/CHEBI_28775|http://purl.obolibrary.org/obo/CHEBI_61606
T367 2390-2400 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T368 2411-2422 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T369 2465-2470 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T370 2606-2610 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T371 2612-2621 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T373 2623-2636 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T374 2643-2646 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T375 2734-2744 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T376 2761-2771 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T377 2833-2844 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T378 2980-2985 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T379 3123-3133 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T380 3146-3157 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T381 3247-3257 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T382 3267-3278 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T383 3864-3873 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T384 3905-3908 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T385 4007-4017 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T386 4048-4051 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T387 4121-4132 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T388 4196-4203 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T389 4463-4473 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T390 4475-4479 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T391 4481-4484 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T392 4498-4507 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T394 4509-4522 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T395 4524-4534 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T396 4665-4672 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T397 4768-4778 Chemical denotes polyphenol http://purl.obolibrary.org/obo/CHEBI_26195
T398 4913-4922 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T399 4992-4999 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T400 5115-5124 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T401 5196-5199 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T402 5260-5263 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T403 5289-5296 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T10 2665-2673 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
571 161-165 Gene denotes TF2b Gene:2959
572 233-237 Gene denotes RdRp Gene:43740578
573 815-819 Gene denotes RdRp Gene:43740578
574 832-836 Gene denotes RdRp Gene:43740578
575 843-847 Gene denotes RdRp Gene:43740578
576 853-857 Gene denotes RdRp Gene:43740578
577 858-862 Gene denotes TF2b Gene:2959
578 864-868 Gene denotes RdRp Gene:43740578
579 875-879 Gene denotes RdRp Gene:43740578
580 891-895 Gene denotes RdRp Gene:43740578
581 911-915 Gene denotes RdRp Gene:43740578
582 932-936 Gene denotes RdRp Gene:43740578
583 1013-1017 Gene denotes RdRp Gene:43740578
584 1030-1034 Gene denotes RdRp Gene:43740578
585 222-232 Species denotes SARS-CoV-2 Tax:2697049
586 132-142 Chemical denotes remdesivir MESH:C000606551
587 144-148 Chemical denotes EGCG MESH:C045651
588 172-182 Chemical denotes hesperidin MESH:D006569
589 184-193 Chemical denotes myricetin MESH:C040015
590 820-830 Chemical denotes remdesivir MESH:C000606551
591 399-413 Disease denotes backbone atoms
593 1431-1445 Disease denotes backbone atoms
604 1819-1823 Gene denotes RdRp Gene:43740578
605 1880-1884 Gene denotes RdRp Gene:43740578
606 1989-1993 Gene denotes RdRp Gene:43740578
607 1994-1998 Gene denotes TF2b Gene:2959
608 2044-2048 Gene denotes RdRp Gene:43740578
609 2049-2056 Gene denotes TF2a 1 Gene:2957
610 2100-2104 Gene denotes RdRp Gene:43740578
611 2161-2165 Gene denotes RdRp Gene:43740578
612 2225-2229 Gene denotes RdRp Gene:43740578
613 1824-1834 Chemical denotes Remdesivir MESH:C000606551
623 2752-2756 Gene denotes TF2b Gene:2959
624 2390-2400 Chemical denotes remdesivir MESH:C000606551
625 2411-2422 Chemical denotes polyphenols MESH:D059808
626 2606-2610 Chemical denotes EGCG MESH:C045651
627 2612-2621 Chemical denotes myricetin MESH:C040015
628 2623-2636 Chemical denotes quercetagetin MESH:C079163
629 2734-2744 Chemical denotes remdesivir MESH:C000606551
630 2761-2771 Chemical denotes hesperidin MESH:D006569
631 2833-2844 Chemical denotes polyphenols MESH:D059808
652 3194-3198 Gene denotes RdRp Gene:43740578
653 3242-3246 Gene denotes RdRp Gene:43740578
654 3262-3266 Gene denotes RdRp Gene:43740578
655 3859-3863 Gene denotes RdRp Gene:43740578
656 3900-3904 Gene denotes RdRp Gene:43740578
657 3913-3917 Gene denotes RdRp Gene:43740578
658 4002-4006 Gene denotes RdRp Gene:43740578
659 4087-4091 Gene denotes RdRp Gene:43740578
660 3398-3399 Gene denotes N Gene:43740575
661 3123-3133 Chemical denotes remdesivir MESH:C000606551
662 3146-3157 Chemical denotes polyphenols MESH:D059808
663 3247-3257 Chemical denotes remdesivir MESH:C000606551
664 3267-3278 Chemical denotes polyphenols MESH:D059808
665 3441-3447 Chemical denotes Asn150
666 3449-3455 Chemical denotes Asp260
667 3457-3463 Chemical denotes Arg305
668 3465-3471 Chemical denotes Asn360
669 3477-3483 Chemical denotes Phe440
670 4007-4017 Chemical denotes polyphenol MESH:D059808
671 4121-4132 Chemical denotes polyphenols MESH:D059808
685 4443-4447 Gene denotes RdRp Gene:43740578
686 4486-4490 Gene denotes TF2b Gene:2959
687 4763-4767 Gene denotes RdRp Gene:43740578
688 5065-5069 Gene denotes RdRp Gene:43740578
689 5070-5074 Gene denotes TF2b Gene:2959
690 5110-5114 Gene denotes RdRp Gene:43740578
691 4463-4473 Chemical denotes remdesivir MESH:C000606551
692 4475-4479 Chemical denotes EGCG MESH:C045651
693 4498-4507 Chemical denotes myricetin MESH:C040015
694 4509-4522 Chemical denotes quercetagetin MESH:C079163
695 4524-4534 Chemical denotes hesperidin MESH:D006569
696 4768-4778 Chemical denotes polyphenol MESH:D059808
697 4948-4952 Chemical denotes SASA

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T9 150-153 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T10 937-940 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T11 2291-2294 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T12 2638-2641 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T13 4539-4542 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T230 0-6 Sentence denotes 3.2.1.
T231 8-56 Sentence denotes Thermodynamic stability and flexibility analysis
T232 57-341 Sentence denotes The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes.
T233 342-523 Sentence denotes Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A).
T234 524-691 Sentence denotes It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium.
T235 692-975 Sentence denotes The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3).
T236 976-1077 Sentence denotes The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation.
T237 1078-1299 Sentence denotes We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information).
T238 1300-1358 Sentence denotes Overall, this suggests the convergence of our simulations.
T239 1359-1582 Sentence denotes Figure 3. (A) Time evolution of root-mean-square deviations (RMSDs) of backbone atoms and (B) the root-mean-square fluctuations (RMSFs) of Cα atoms of nine complexes relative to their respective energy minimized structure.
T240 1583-1591 Sentence denotes Table 3.
T241 1593-1712 Sentence denotes The average backbone RMSD, radius of gyration (RoG), and solvent accessible surface area (SASA) for all nine complexes.
T242 1713-1781 Sentence denotes The data are reported as average ± standard error of the mean (SEM).
T243 1782-1818 Sentence denotes System RMSD (Å) RoG (Å) SASA (Å2)
T244 1819-1879 Sentence denotes RdRp/Remdesivir 2.30 ± 0.03 29.96 ± 0.02 34973.20 ± 91.56
T245 1880-1934 Sentence denotes RdRp/EGCG 2.45 ± 0.05 29.52 ± 0.06 35026.03 ± 63.52
T246 1935-1988 Sentence denotes RdRp/TF3 1.87 ± 0.02 29.60 ± 0.01 34080.16 ± 53.41
T247 1989-2043 Sentence denotes RdRp/TF2b 2.28 ± 0.01 29.86 ± 0.02 35462.92 ± 50.40
T248 2044-2099 Sentence denotes RdRp/TF2a 1.68 ± 0.02 29.75 ± 0.02 34312.55 ± 112.89
T249 2100-2160 Sentence denotes RdRp/Myricetin 2.47 ± 0.03 29.88 ± 0.01 35395.35 ± 104.67
T250 2161-2224 Sentence denotes RdRp/Quercetagetin 1.90 ± 0.03 29.84 ± 0.01 34618.65 ± 51.25
T251 2225-2285 Sentence denotes RdRp/Hesperidin 2.03 ± 0.04 29.74 ± 0.02 34554.08 ± 47.25
T252 2286-2570 Sentence denotes RdRp/TF1 1.88 ± 0.03 29.86 ± 0.01 34420.69 ± 56.90 Next, we investigated the structural stability of remdesivir and eight polyphenols by estimating the temporal RMSDs of heavy atoms relative to their respective initial coordinates (see Figure S2B in the Supplementary Information).
T253 2571-2724 Sentence denotes It is evident from Figure S2B that EGCG, myricetin, quercetagetin, TF1, TF3 displayed a rigid behavior in the bound form with an average RMSD of < 1.0 Å.
T254 2725-2887 Sentence denotes However, remdesivir, TF2a, TF2b and hesperidin showed higher fluctuations as compared to the abovementioned polyphenols, and an average RMSD of > 2.0 Å was noted.
T255 2888-3042 Sentence denotes To identify the regions which are flexible, the root-mean-square fluctuations (RMSFs) of Cα atoms of each residue are calculated and shown in Figure 3(B).
T256 3043-3214 Sentence denotes From this analysis, we can get a better insight into what extent the binding of remdesivir and natural polyphenols affects the residual flexibility of RdRp (mainly Nsp12).
T257 3215-3309 Sentence denotes Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern.
T258 3310-3425 Sentence denotes Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal.
T259 3426-3559 Sentence denotes Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes.
T260 3560-3884 Sentence denotes The binding pocket residues, such as Asp452, Lys545, Lys551, Tyr455, Arg553, Ala554, Arg555, Thr556, Asp618, Tyr619, pro620, Lys621, Cys622, Asp623 Arg624, Asn691, Asp760, Asp761, Phe793, Met794, Ser795, Lys798, Trp800, Glu811, Phe812, and Ser814 exhibited considerably low fluctuations for all the RdRp-inhibitor complexes.
T261 3885-4028 Sentence denotes In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes.
T262 4029-4133 Sentence denotes This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols.
T263 4134-4325 Sentence denotes Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information.
T264 4326-4566 Sentence denotes The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3).
T265 4567-4651 Sentence denotes This suggests that the structural compactness remained unchanged during simulations.
T266 4652-4846 Sentence denotes Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information.
T267 4847-4898 Sentence denotes The average values of SASA are reported in Table 3.
T268 4899-5010 Sentence denotes Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure.
T269 5011-5135 Sentence denotes Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes.
T270 5136-5213 Sentence denotes On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2).
T271 5214-5307 Sentence denotes Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion.