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PMC:7441777 / 8804-13859 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T26 41-48 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T27 160-167 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 4461-4468 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T29 4522-4529 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 4741-4748 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T43 87-95 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 572-580 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 715-723 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 1269-1277 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 3863-3871 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 4183-4191 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T64 844-846 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T65 1438-1440 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T66 1497-1500 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T67 1679-1680 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T68 1818-1820 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T69 1984-1985 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T70 2127-2129 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T71 2241-2243 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T72 2310-2312 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T73 2538-2540 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T74 2863-2865 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T75 2877-2878 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T76 2912-2914 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T77 2958-2960 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T78 3211-3213 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T79 3317-3319 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T80 3377-3379 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T81 3391-3392 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T82 3529-3531 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T83 3672-3675 http://purl.obolibrary.org/obo/CLO_0054060 denotes 102
T84 3982-3983 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 4113-4114 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T86 4128-4129 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T87 4135-4136 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T88 4142-4143 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T89 4158-4161 http://purl.obolibrary.org/obo/CLO_0001053 denotes 121
T90 4173-4174 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T91 4554-4555 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T103 41-48 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T104 108-110 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T105 160-167 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T106 273-281 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T107 282-287 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T108 553-563 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T109 698-707 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T110 783-786 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T112 788-798 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T113 821-832 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T114 1183-1194 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T115 1229-1232 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T117 1237-1247 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T118 1285-1287 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T119 1426-1429 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T120 1442-1450 Chemical denotes Cyanidin http://purl.obolibrary.org/obo/CHEBI_27843
T121 1478-1486 Chemical denotes Daidzein http://purl.obolibrary.org/obo/CHEBI_28197
T122 1550-1557 Chemical denotes Wogonin http://purl.obolibrary.org/obo/CHEBI_10043
T123 1568-1578 Chemical denotes Hesperidin http://purl.obolibrary.org/obo/CHEBI_28775|http://purl.obolibrary.org/obo/CHEBI_61606
T125 1591-1600 Chemical denotes Phloretin http://purl.obolibrary.org/obo/CHEBI_17276
T126 1611-1615 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T127 1647-1656 Chemical denotes Myricetin http://purl.obolibrary.org/obo/CHEBI_18152
T128 1691-1704 Chemical denotes Quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T129 1737-1746 Chemical denotes Quercetin http://purl.obolibrary.org/obo/CHEBI_16243
T130 1758-1768 Chemical denotes Pinosylvin http://purl.obolibrary.org/obo/CHEBI_36011
T131 1779-1787 Chemical denotes Curcumin http://purl.obolibrary.org/obo/CHEBI_3962
T132 1799-1811 Chemical denotes Formononetin http://purl.obolibrary.org/obo/CHEBI_18088
T133 1850-1864 Chemical denotes Liquiritigenin http://purl.obolibrary.org/obo/CHEBI_28777
T134 1875-1883 Chemical denotes Peonidin http://purl.obolibrary.org/obo/CHEBI_75033
T135 1895-1903 Chemical denotes Prunetin http://purl.obolibrary.org/obo/CHEBI_8600
T136 1914-1921 Chemical denotes Fisetin http://purl.obolibrary.org/obo/CHEBI_42567
T137 1974-1985 Chemical denotes Biochanin A http://purl.obolibrary.org/obo/CHEBI_17574
T138 2047-2057 Chemical denotes Kaempferol http://purl.obolibrary.org/obo/CHEBI_28499
T139 2069-2078 Chemical denotes Genistein http://purl.obolibrary.org/obo/CHEBI_27514|http://purl.obolibrary.org/obo/CHEBI_28088
T141 2089-2101 Chemical denotes Scutellarein http://purl.obolibrary.org/obo/CHEBI_9062
T142 2158-2174 Chemical denotes 6-Hydroxyflavone http://purl.obolibrary.org/obo/CHEBI_34472
T143 2185-2193 Chemical denotes Purpurin http://purl.obolibrary.org/obo/CHEBI_8645
T144 2205-2210 Chemical denotes Equol http://purl.obolibrary.org/obo/CHEBI_34741
T145 2221-2233 Chemical denotes Isorhamnetin http://purl.obolibrary.org/obo/CHEBI_6052
T146 2245-2256 Chemical denotes Piceatannol http://purl.obolibrary.org/obo/CHEBI_28814
T147 2267-2275 Chemical denotes Tricetin http://purl.obolibrary.org/obo/CHEBI_507499
T148 2314-2324 Chemical denotes Gossypetin http://purl.obolibrary.org/obo/CHEBI_16400
T149 2336-2347 Chemical denotes Resveratrol http://purl.obolibrary.org/obo/CHEBI_27881|http://purl.obolibrary.org/obo/CHEBI_45713
T151 2358-2369 Chemical denotes Norathyriol http://purl.obolibrary.org/obo/CHEBI_7622
T152 2401-2411 Chemical denotes Coumestrol http://purl.obolibrary.org/obo/CHEBI_3908
T153 2441-2455 Chemical denotes Isosakuranetin http://purl.obolibrary.org/obo/CHEBI_27552
T154 2475-2479 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T155 2518-2531 Chemical denotes Pterostilbene http://purl.obolibrary.org/obo/CHEBI_8630
T156 2564-2576 Chemical denotes Ferulic acid http://purl.obolibrary.org/obo/CHEBI_17620
T157 2572-2576 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T158 2608-2620 Chemical denotes Caffeic acid http://purl.obolibrary.org/obo/CHEBI_16433|http://purl.obolibrary.org/obo/CHEBI_17395
T160 2616-2620 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T161 2631-2641 Chemical denotes Pratensein http://purl.obolibrary.org/obo/CHEBI_8359
T162 2664-2668 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T163 2679-2689 Chemical denotes Hispidulin http://purl.obolibrary.org/obo/CHEBI_75902
T164 2716-2720 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T165 2731-2740 Chemical denotes Baicalein http://purl.obolibrary.org/obo/CHEBI_2979
T166 2752-2765 Chemical denotes Gentisic acid http://purl.obolibrary.org/obo/CHEBI_17189
T167 2761-2765 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T168 2776-2784 Chemical denotes Apigenin http://purl.obolibrary.org/obo/CHEBI_18388
T169 2796-2806 Chemical denotes Pyrogallol http://purl.obolibrary.org/obo/CHEBI_16164
T170 2834-2856 Chemical denotes 4-Hydroxycinnamic acid http://purl.obolibrary.org/obo/CHEBI_32374
T171 2852-2856 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T172 2890-2905 Chemical denotes Resacetophenone http://purl.obolibrary.org/obo/CHEBI_18414
T173 2916-2924 Chemical denotes Acacetin http://purl.obolibrary.org/obo/CHEBI_15335
T174 2947-2951 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T175 2962-2974 Chemical denotes Pelargonidin http://purl.obolibrary.org/obo/CHEBI_28510
T176 2995-2999 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T177 3010-3017 Chemical denotes Irilone http://purl.obolibrary.org/obo/CHEBI_5970
T178 3046-3050 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T179 3061-3071 Chemical denotes Naringenin http://purl.obolibrary.org/obo/CHEBI_17846
T180 3083-3094 Chemical denotes Gallic acid http://purl.obolibrary.org/obo/CHEBI_30778
T181 3090-3094 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T182 3128-3149 Chemical denotes 3-Hydroxybenzoic acid http://purl.obolibrary.org/obo/CHEBI_30764
T183 3145-3149 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T184 3160-3171 Chemical denotes Kaempferide http://purl.obolibrary.org/obo/CHEBI_6099
T185 3183-3204 Chemical denotes 4-Hydroxybenzoic acid http://purl.obolibrary.org/obo/CHEBI_30763
T186 3200-3204 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T187 3215-3223 Chemical denotes Malvidin http://purl.obolibrary.org/obo/CHEBI_6674
T188 3235-3243 Chemical denotes Vanillin http://purl.obolibrary.org/obo/CHEBI_18346
T189 3254-3262 Chemical denotes Luteolin http://purl.obolibrary.org/obo/CHEBI_15864
T190 3285-3289 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T191 3300-3309 Chemical denotes Dalbergin http://purl.obolibrary.org/obo/CHEBI_4308
T192 3321-3334 Chemical denotes Vanillic acid http://purl.obolibrary.org/obo/CHEBI_30816
T193 3330-3334 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T194 3345-3351 Chemical denotes Butein http://purl.obolibrary.org/obo/CHEBI_3237
T195 3363-3370 Chemical denotes Paeonol http://purl.obolibrary.org/obo/CHEBI_69581
T196 3381-3392 Chemical denotes Biochanin A http://purl.obolibrary.org/obo/CHEBI_17574
T197 3409-3422 Chemical denotes Cinnamic acid http://purl.obolibrary.org/obo/CHEBI_27386
T198 3418-3422 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T199 3433-3439 Chemical denotes Fustin http://purl.obolibrary.org/obo/CHEBI_5202
T200 3451-3470 Chemical denotes Protocatechuic acid http://purl.obolibrary.org/obo/CHEBI_36062
T201 3466-3470 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T202 3509-3522 Chemical denotes 4-Ethylphenol http://purl.obolibrary.org/obo/CHEBI_49584
T203 3556-3564 Chemical denotes Catechol http://purl.obolibrary.org/obo/CHEBI_18135
T204 3599-3606 Chemical denotes Tyrosol http://purl.obolibrary.org/obo/CHEBI_1879
T205 3641-3644 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T207 3656-3664 Chemical denotes Galangin http://purl.obolibrary.org/obo/CHEBI_5262
T208 3791-3802 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T209 3804-3814 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T210 3820-3823 Chemical denotes GTP http://purl.obolibrary.org/obo/CHEBI_15996|http://purl.obolibrary.org/obo/CHEBI_37565
T212 3928-3934 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T213 4031-4035 Chemical denotes atom http://purl.obolibrary.org/obo/CHEBI_33250
T214 4057-4064 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T215 4256-4262 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T216 4405-4411 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T217 4412-4420 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T218 4461-4468 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T219 4469-4475 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T220 4522-4529 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T221 4530-4536 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T222 4741-4748 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T223 4749-4755 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T224 4859-4867 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T225 4901-4905 Chemical denotes atom http://purl.obolibrary.org/obo/CHEBI_33250

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
302 98-102 Gene denotes RdRp Gene:43740578
303 583-587 Gene denotes RdRp Gene:43740578
304 342-346 Gene denotes v4.2 Gene:28781
305 87-97 Species denotes SARS-CoV-2 Tax:2697049
306 572-582 Species denotes SARS-CoV-2 Tax:2697049
307 273-281 Chemical denotes hydrogen MESH:D006859
310 726-730 Gene denotes RdRp Gene:43740578
311 715-725 Species denotes SARS-CoV-2 Tax:2697049
315 783-786 Chemical denotes GTP MESH:D006160
316 788-798 Chemical denotes remdesivir MESH:C000606551
317 821-832 Chemical denotes polyphenols MESH:D059808
322 1461-1465 Gene denotes TF2b Gene:2959
323 1373-1374 Gene denotes S Gene:43740568
324 1323-1324 Gene denotes S Gene:43740568
325 3678-3688 Chemical denotes Remdesivir MESH:C000606551
331 1257-1261 Gene denotes RdRp Gene:43740578
332 1269-1279 Species denotes SARS-CoV-2 Tax:2697049
333 1183-1194 Chemical denotes polyphenols MESH:D059808
334 1229-1232 Chemical denotes GTP MESH:D006160
335 1237-1247 Chemical denotes remdesivir MESH:C000606551
343 3855-3859 Gene denotes RdRp Gene:43740578
344 4194-4198 Gene denotes RdRp Gene:43740578
345 3863-3873 Species denotes SARS-CoV-2 Tax:2697049
346 4183-4193 Species denotes SARS-CoV-2 Tax:2697049
347 3791-3802 Chemical denotes polyphenols MESH:D059808
348 3804-3814 Chemical denotes remdesivir MESH:C000606551
349 3820-3823 Chemical denotes GTP MESH:D006160
351 4859-4867 Chemical denotes hydrogen MESH:D006859

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T3 1497-1500 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T62 0-4 Sentence denotes 2.1.
T63 6-31 Sentence denotes Molecular docking studies
T64 33-39 Sentence denotes 2.1.1.
T65 41-61 Sentence denotes Protein preparations
T66 62-111 Sentence denotes The crystal structure of SARS-CoV-2 RdRp (PDB ID:
T67 112-214 Sentence denotes 6M71) (Yan et al., 2020) was retrieved from the protein databank (www.rcsb.org) (Berman et al., 2000).
T68 215-377 Sentence denotes The crystal structure was prepared individually by adding hydrogen atoms and computing the Gasteiger charge using the AutoDock v4.2 program (Morris et al., 2009).
T69 378-465 Sentence denotes Subsequently, the file was saved as .pdbqt format in preparation for molecular docking.
T70 466-609 Sentence denotes Schematic representation of the work-flow for selecting potential natural polyphenolic inhibitors for the SARS-CoV-2 RdRp is shown in Figure 2.
T71 610-619 Sentence denotes Figure 2.
T72 621-731 Sentence denotes Flow chart of the methodology for shortlisting the best natural polyphenolic inhibitor of the SARS-CoV-2 RdRp.
T73 733-739 Sentence denotes 2.1.2.
T74 741-760 Sentence denotes Ligand preparations
T75 761-973 Sentence denotes The SDF structures of GTP, remdesivir, and selected hundred polyphenols (see Table S1 in Supplementary Information) were retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) (Kim et al., 2019).
T76 974-1131 Sentence denotes The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).
T77 1132-1140 Sentence denotes Table 1.
T78 1142-1288 Sentence denotes Binding energy (kcal/mol) of the natural polyphenols along with the control compounds (GTP and remdesivir) against RdRp of the SARS-CoV-2 (PDB ID:
T79 1289-1322 Sentence denotes 6M71) by molecular docking study.
T80 1323-1325 Sentence denotes S.
T81 1326-1329 Sentence denotes No.
T82 1331-1375 Sentence denotes Compound Name Binding energy (kcal/mol) S.
T83 1376-1379 Sentence denotes No.
T84 1381-1421 Sentence denotes Compound Name Binding energy (kcal/mol)
T85 1422-1456 Sentence denotes 1 TF3 −9.9 52 Cyanidin −6.3
T86 1457-1492 Sentence denotes 2 TF2b −9.6 53 Daidzein −6.3
T87 1493-1528 Sentence denotes 3 TF1 −9.6 54 Glycitein −6.3
T88 1529-1563 Sentence denotes 4 TF2a −9.3 55 Wogonin −6.3
T89 1564-1606 Sentence denotes 5 Hesperidin −8.8 56 Phloretin −6.3
T90 1607-1642 Sentence denotes 6 EGCG −7.3 57 Catechin −6.2
T91 1643-1686 Sentence denotes 7 Myricetin −7.2 58 Urolithin B −6.2
T92 1687-1733 Sentence denotes 8 Quercetagetin −7.0 59 Angolensin −6.2
T93 1734-1774 Sentence denotes 9 Quercetin −6.9 60 Pinosylvin −6.2
T94 1775-1817 Sentence denotes 10 Curcumin −6.9 61 Formononetin −6.2
T95 1818-1870 Sentence denotes 11 Dihydrorobinetin −6.8 62 Liquiritigenin −6.2
T96 1871-1909 Sentence denotes 12 Peonidin −6.8 63 Prunetin −6.2
T97 1910-1948 Sentence denotes 13 Fisetin −6.8 64 Alpinetin −6.2
T98 1949-1991 Sentence denotes 14 Robinetin −6.7 65 Biochanin A −6.2
T99 1992-2042 Sentence denotes 15 5-Deoxygalangin −6.7 66 Rhapontigenin −6.1
T100 2043-2084 Sentence denotes 16 Kaempferol −6.7 67 Genistein −6.1
T101 2085-2126 Sentence denotes 17 Scutellarein −6.7 68 Chrysin −6.1
T102 2127-2180 Sentence denotes 18 (-)-Epicatechin −6.7 69 6-Hydroxyflavone −6.1
T103 2181-2216 Sentence denotes 19 Purpurin −6.7 70 Equol −6.1
T104 2217-2262 Sentence denotes 20 Isorhamnetin −6.7 71 Piceatannol −6.1
T105 2263-2309 Sentence denotes 21 Tricetin −6.6 72 Isorhapontigenin −6.0
T106 2310-2353 Sentence denotes 22 Gossypetin −6.6 73 Resveratrol −5.8
T107 2354-2396 Sentence denotes 23 Norathyriol −6.6 74 Danshensu −5.7
T108 2397-2436 Sentence denotes 24 Coumestrol −6.6 75 Eugenin −5.6
T109 2437-2485 Sentence denotes 25 Isosakuranetin −6.6 76 Sinapic acid −5.5
T110 2486-2537 Sentence denotes 26 Pectolinarigenin −6.6 77 Pterostilbene −5.5
T111 2538-2582 Sentence denotes 27 Tangeritin −6.6 78 Ferulic acid −5.4
T112 2583-2626 Sentence denotes 28 Nobiletin −6.6 79 Caffeic acid −5.4
T113 2627-2674 Sentence denotes 29 Pratensein −6.6 80 Isoferulic acid −5.4
T114 2675-2726 Sentence denotes 30 Hispidulin −6.6 81 Dihydrocaffeic acid −5.4
T115 2727-2771 Sentence denotes 31 Baicalein −6.5 82 Gentisic acid −5.3
T116 2772-2812 Sentence denotes 32 Apigenin −6.5 83 Pyrogallol −5.3
T117 2813-2862 Sentence denotes 33 Morin −6.5 84 4-Hydroxycinnamic acid −5.2
T118 2863-2911 Sentence denotes 34 Urolithin A −6.5 85 Resacetophenone −5.2
T119 2912-2957 Sentence denotes 35 Acacetin −6.5 86 Salicyclic acid −5.1
T120 2958-3005 Sentence denotes 36 Pelargonidin −6.5 87 Syringic acid −5.1
T121 3006-3056 Sentence denotes 37 Irilone −6.5 88 2-Hydroxybenzoic acid −5.1
T122 3057-3100 Sentence denotes 38 Naringenin −6.5 89 Gallic acid −5.0
T123 3101-3155 Sentence denotes 39 Pinocembrin −6.5 90 3-Hydroxybenzoic acid −5.0
T124 3156-3210 Sentence denotes 40 Kaempferide −6.5 91 4-Hydroxybenzoic acid −5.0
T125 3211-3249 Sentence denotes 41 Malvidin −6.5 92 Vanillin −5.0
T126 3250-3295 Sentence denotes 42 Luteolin −6.4 93 p-Coumeric acid −4.9
T127 3296-3340 Sentence denotes 43 Dalbergin −6.4 94 Vanillic acid −4.8
T128 3341-3376 Sentence denotes 44 Butein −6.4 95 Paeonol −4.8
T129 3377-3428 Sentence denotes 45 Biochanin A (1-) −6.4 96 Cinnamic acid −4.7
T130 3429-3476 Sentence denotes 46 Fustin −6.4 97 Protocatechuic acid −4.6
T131 3477-3528 Sentence denotes 47 5-Hydroxyflavone −6.4 98 4-Ethylphenol −4.5
T132 3529-3570 Sentence denotes 48 Pinostrobin −6.4 99 Catechol −4.5
T133 3571-3612 Sentence denotes 49 Pinobanksin −6.4 100 Tyrosol −4.5
T134 3613-3651 Sentence denotes 50 Datiscetin −6.3 101 GTP −7.9
T135 3652-3695 Sentence denotes 51 Galangin −6.3 102 Remdesivir −7.7
T136 3697-3703 Sentence denotes 2.1.3.
T137 3705-3740 Sentence denotes Docking studies using AutoDock Vina
T138 3741-3923 Sentence denotes The energy-minimized structure of all the natural polyphenols, remdesivir, and GTP were docked with the receptor (RdRp of SARS-CoV-2) using AutoDock Vina 1.1.2 (Trott & Olson, 2010).
T139 3924-4112 Sentence denotes The ligand files were further saved in PDBQT file format, a modified PDB format containing atomic charges, atom type definitions for ligands, and topological information (rotatable bonds).
T140 4113-4236 Sentence denotes A grid box (30 Å × 30 Å × 30 Å) centered at (121, 120, 125) Å for the SARS-CoV-2 RdRp, was used in the docking experiments.
T141 4237-4326 Sentence denotes After the receptor-ligand preparation, docking runs were started from the command prompt.
T142 4327-4451 Sentence denotes The lowest binding energy and best-docked conformation were considered as the ligand molecule with maximum binding affinity.
T143 4453-4459 Sentence denotes 2.1.4.
T144 4461-4488 Sentence denotes Protein-ligand interactions
T145 4489-4672 Sentence denotes LigPlot+ was used to investigate protein-ligand interactions for a given .pdb file containing the docked conformation and also the final simulated conformation (Wallace et al., 1995).
T146 4673-4768 Sentence denotes The LigPlot+ program self-generated schematic 2D representations of protein-ligand interaction.
T147 4769-4922 Sentence denotes The output file represents the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic contacts, and atom accessibilities.
T148 4923-5055 Sentence denotes H-bonds are shown in green dotted lines, whereas residues involved in hydrophobic interaction are represented in the red semicircle.

2_test

Id Subject Object Predicate Lexical cue
32720577-19399780-56195101 371-375 19399780 denotes 2009
32720577-30371825-56195102 967-971 30371825 denotes 2019
32720577-15264254-56195103 1125-1129 15264254 denotes 2004
32720577-7630882-56195104 4666-4670 7630882 denotes 1995