> top > docs > PMC:7279430 > spans > 21817-24286 > annotations

PMC:7279430 / 21817-24286 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T49 481-488 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T50 520-527 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T51 830-833 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T52 844-847 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T53 889-896 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T54 1166-1172 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T55 1218-1225 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T56 1303-1310 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T57 1393-1400 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T58 1484-1491 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T59 1526-1533 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T60 1621-1628 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T61 1768-1775 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T62 1810-1817 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
904 883-888 Gene denotes spike Gene:43740568
905 961-990 Gene denotes angiotensin-converting enzyme Gene:1636
906 1297-1302 Gene denotes spike Gene:43740568
907 1321-1325 Gene denotes ACE2 Gene:59272
908 1387-1392 Gene denotes spike Gene:43740568
909 1405-1409 Gene denotes ACE2 Gene:59272
910 1424-1428 Gene denotes ACE2 Gene:59272
911 1478-1483 Gene denotes spike Gene:43740568
912 1520-1525 Gene denotes spike Gene:43740568
913 1579-1583 Gene denotes ACE2 Gene:59272
914 2191-2200 Gene denotes Edock/MW⅓
915 500-510 Species denotes SARS-CoV-2 Tax:2697049
916 632-642 Species denotes SARS-CoV-2 Tax:2697049
917 722-732 Species denotes SARS-CoV-2 Tax:2697049
918 763-773 Species denotes SARS-CoV-2 Tax:2697049
919 819-829 Species denotes SARS-CoV-2 Tax:2697049
920 872-882 Species denotes SARS-CoV-2 Tax:2697049
921 955-960 Species denotes human Tax:9606
922 1315-1320 Species denotes human Tax:9606
923 381-398 Chemical denotes bicyclogermacrene
924 400-411 Chemical denotes costunolide MESH:C002602
925 413-421 Chemical denotes curdione MESH:C504126
926 423-435 Chemical denotes germacrene D MESH:C027259
927 437-447 Chemical denotes germacrone MESH:C048393
928 453-463 Chemical denotes α-humulene MESH:C042686
929 804-807 CellLine denotes W01 CVCL:6008

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T122 500-508 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T123 632-640 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T124 722-730 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T125 763-771 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T126 819-827 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T127 872-880 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T156 50-52 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T157 466-467 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T158 560-561 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 955-960 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T160 1159-1163 http://purl.obolibrary.org/obo/CLO_0001557 denotes a 15
T161 1164-1165 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T162 1315-1320 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T163 1788-1789 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 1995-1996 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 2323-2324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T350 5-11 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T351 140-147 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T352 381-398 Chemical denotes bicyclogermacrene http://purl.obolibrary.org/obo/CHEBI_63709
T353 400-411 Chemical denotes costunolide http://purl.obolibrary.org/obo/CHEBI_3900
T354 423-435 Chemical denotes germacrene D http://purl.obolibrary.org/obo/CHEBI_49045
T355 423-433 Chemical denotes germacrene http://purl.obolibrary.org/obo/CHEBI_36743
T356 455-463 Chemical denotes humulene http://purl.obolibrary.org/obo/CHEBI_49289
T357 481-488 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T358 520-527 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T359 774-784 Chemical denotes ADP ribose http://purl.obolibrary.org/obo/CHEBI_16960
T360 774-777 Chemical denotes ADP http://purl.obolibrary.org/obo/CHEBI_16761|http://purl.obolibrary.org/obo/CHEBI_456216|http://purl.obolibrary.org/obo/CHEBI_73342
T363 778-784 Chemical denotes ribose http://purl.obolibrary.org/obo/CHEBI_33942|http://purl.obolibrary.org/obo/CHEBI_47013
T365 889-896 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T366 961-972 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T367 1218-1225 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T368 1260-1266 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T369 1303-1310 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T370 1393-1400 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T371 1484-1491 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T372 1526-1533 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T373 1621-1628 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T374 1768-1775 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T375 1810-1817 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T376 1839-1845 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T377 1923-1930 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T378 2026-2032 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T379 2197-2199 Chemical denotes MW http://purl.obolibrary.org/obo/CHEBI_74709
T380 2284-2286 Chemical denotes MW http://purl.obolibrary.org/obo/CHEBI_74709

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T15 481-496 http://purl.obolibrary.org/obo/GO_0006605 denotes protein targets
T16 785-796 http://purl.obolibrary.org/obo/GO_0016791 denotes phosphatase

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T152 0-55 Sentence denotes Each ligand structure was prepared using Spartan ’18 v.
T153 56-100 Sentence denotes 1.4.4 (Wavefunction, Inc., Irvine, CA, USA).
T154 101-221 Sentence denotes The lowest-energy conformations of the ligands were determined and used as starting structures in the molecular docking.
T155 222-465 Sentence denotes This is particularly important to include all potential conformations in medium-sized rings where interconversion between conformations may be hindered (e.g., bicyclogermacrene, costunolide, curdione, germacrene D, germacrone, and α-humulene).
T156 466-662 Sentence denotes A total of six protein targets of SARS-CoV-2 from the Protein Data Bank (PDB), represented by a total of 17 structures, were used in the molecular docking, including SARS-CoV-2 main protease (PDB:
T157 663-755 Sentence denotes 5R7Z, 5R80, 5R81, 5R82, 5R83, 5R84, 6LU7, 6M03, and 6Y84), SARS-CoV-2 endoribonuclease (PDB:
T158 756-802 Sentence denotes 6VWW), SARS-CoV-2 ADP ribose phosphatase (PDB:
T159 803-864 Sentence denotes 6W01 and 6W02), SARS-CoV-2 RNA-dependent RNA polymerase (PDB:
T160 865-917 Sentence denotes 6M71), SARS-CoV-2 spike protein binding domain (PDB:
T161 918-996 Sentence denotes 6M0J, 6VX1, 6VW1, and 6M17), and the human angiotensin-converting enzyme (PDB:
T162 997-1025 Sentence denotes 6M0J, 6VX1, 6VW1, and 6M17).
T163 1026-1091 Sentence denotes Molecular docking was carried out using Molegro Virtual Docker v.
T164 1092-1149 Sentence denotes 6.0.1 (Aarhus, Denmark) as previously reported [128,129].
T165 1150-1277 Sentence denotes Briefly, a 15-Å radius sphere centered on the binding sites of each protein structure in order to permit each ligand to search.
T166 1278-1410 Sentence denotes In the case of the spike protein and human ACE2, the docking sphere was located at the interface between the spike protein and ACE2.
T167 1411-1584 Sentence denotes In one case, ACE2 was removed and docking was carried out with the spike protein, and in the other case, the spike protein was removed and docking was carried out with ACE2.
T168 1585-1762 Sentence denotes Standard protonation states of each protein, based on neutral pH, were used, and charges were assigned based on standard templates as part of the Molegro Virtual Docker program.
T169 1763-1829 Sentence denotes Each protein was used as a rigid model without protein relaxation.
T170 1830-1892 Sentence denotes Flexible-ligand models were used in the docking optimizations.
T171 1893-1994 Sentence denotes Different orientations of the ligands were searched and ranked based on their “rerank” energy scores.
T172 1995-2049 Sentence denotes A minimum of 100 runs for each ligand was carried out.
T173 2050-2417 Sentence denotes In analyzing the docking scores, we accounted for the recognized bias due to molecular weight [130,131,132] using the scheme: DSnorm = 7.2 × Edock/MW⅓, where DSnorm is the normalized docking score, Edock is the MolDock re-rank score, MW is the molecular weight, and 7.2 is a scaling constant to ensure the average DSnorm values are comparable to those of Edock [128].
T174 2418-2469 Sentence denotes The best docking results are summarized in Table 1.

2_test

Id Subject Object Predicate Lexical cue
32408699-12546562-52981879 2145-2148 12546562 denotes 130
32408699-15214778-52981880 2149-2152 15214778 denotes 131
32408699-17552493-52981881 2153-2156 17552493 denotes 132
T24519 2145-2148 12546562 denotes 130
T68906 2149-2152 15214778 denotes 131
T21934 2153-2156 17552493 denotes 132