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PMC:7278709 / 29748-31621 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T61 628-639 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T62 741-752 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T63 809-820 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T64 1183-1194 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T65 1312-1323 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T585 589-595 CHEBI:52217;CHEBI:52217 denotes agents
T586 640-646 CHEBI:17089;CHEBI:17089 denotes glycan
T587 647-659 SO:0000409 denotes binding site
T588 665-670 NCBITaxon:10239 denotes virus
T589 741-747 CHEBI:30563;CHEBI:30563 denotes sialic
T590 748-752 CHEBI:41865;CHEBI:41865 denotes acid
T591 753-759 CHEBI:17089;CHEBI:17089 denotes glycan
T592 809-815 CHEBI:30563;CHEBI:30563 denotes sialic
T593 829-835 SO:0000417 denotes domain
T594 863-875 SO:0000409 denotes target sites
T595 926-938 SO:0000409 denotes target sites
T597 1183-1189 SO:0001707 denotes sialic
T598 1190-1199 SO:0000235 denotes acid site
T599 1200-1207 SO:0001429 denotes binding
T600 1208-1214 SO:0000235 denotes region
T703 1362-1363 SO:0000409 denotes u
T704 1365-1366 SO:0000409 denotes s

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T204 58-68 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T205 191-201 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T206 1073-1083 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T207 1162-1172 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T208 1263-1273 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T209 1332-1342 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T210 1428-1435 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T211 1453-1461 Body_part denotes cysteine http://purl.org/sig/ont/fma/fma82751
T212 1476-1479 Body_part denotes V 1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T214 1484-1497 Body_part denotes aspartic acid http://purl.org/sig/ont/fma/fma82760
T215 1506-1519 Body_part denotes glutamic acid http://purl.org/sig/ont/fma/fma82762
T216 1531-1544 Body_part denotes phenylalanine http://purl.org/sig/ont/fma/fma82754
T217 1559-1566 Body_part denotes glycine http://purl.org/sig/ont/fma/fma82753
T218 1578-1587 Body_part denotes histidine http://purl.org/sig/ont/fma/fma82755
T219 1599-1609 Body_part denotes isoleucine http://purl.org/sig/ont/fma/fma82756
T220 1621-1627 Body_part denotes lysine http://purl.org/sig/ont/fma/fma82758
T221 1639-1646 Body_part denotes leucine http://purl.org/sig/ont/fma/fma82757
T222 1658-1668 Body_part denotes methionine http://purl.org/sig/ont/fma/fma82759
T223 1708-1715 Body_part denotes proline http://purl.org/sig/ont/fma/fma82761
T224 1724-1733 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T225 1745-1753 Body_part denotes arginine http://purl.org/sig/ont/fma/fma82763
T226 1765-1771 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T227 1783-1792 Body_part denotes threonine http://purl.org/sig/ont/fma/fma82765
T228 1807-1813 Body_part denotes valine http://purl.org/sig/ont/fma/fma82766
T229 1828-1838 Body_part denotes tryptophan http://purl.org/sig/ont/fma/fma82767
T230 1853-1861 Body_part denotes tyrosine http://purl.org/sig/ont/fma/fma82768

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T313 401-409 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T314 516-517 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T315 663-664 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T316 665-670 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T317 1426-1427 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T318 1436-1440 http://purl.obolibrary.org/obo/CLO_0051456 denotes A, E
T319 1442-1446 http://purl.obolibrary.org/obo/CLO_0009141 denotes S, T
T320 1442-1446 http://purl.obolibrary.org/obo/CLO_0050980 denotes S, T
T321 1447-1450 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T322 1470-1474 http://purl.obolibrary.org/obo/CLO_0009141 denotes S, T
T323 1470-1474 http://purl.obolibrary.org/obo/CLO_0050980 denotes S, T
T324 1478-1481 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T325 1498-1501 http://purl.obolibrary.org/obo/CLO_0002857 denotes E 1
T326 1520-1521 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T327 1551-1554 http://purl.obolibrary.org/obo/CLO_0009701 denotes Y 1
T328 1551-1554 http://purl.obolibrary.org/obo/CLO_0051608 denotes Y 1
T329 1567-1571 http://purl.obolibrary.org/obo/CLO_0008192 denotes N, P
T330 1572-1575 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T331 1591-1596 http://purl.obolibrary.org/obo/CLO_0008701 denotes R 1 2
T332 1702-1705 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T333 1734-1738 http://purl.obolibrary.org/obo/CLO_0008149 denotes N, E
T334 1772-1773 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T335 1777-1780 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T336 1793-1794 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T337 1799-1802 http://purl.obolibrary.org/obo/CLO_0050050 denotes S 1
T338 1814-1815 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T339 1842-1846 http://purl.obolibrary.org/obo/CLO_0050475 denotes M, Y

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T356 58-68 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T357 58-63 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T358 64-68 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T359 191-201 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T360 191-196 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T361 197-201 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T362 401-409 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T363 428-439 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T364 628-639 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T365 635-639 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T366 741-752 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T367 748-752 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T368 809-820 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T369 816-820 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T370 1073-1083 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T371 1073-1078 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T372 1079-1083 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T373 1162-1172 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T374 1162-1167 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T375 1168-1172 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T376 1183-1194 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T377 1190-1194 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T378 1263-1273 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T379 1269-1273 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T380 1312-1323 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T381 1319-1323 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T382 1332-1342 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T383 1332-1337 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T384 1338-1342 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T385 1428-1435 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T386 1453-1461 Chemical denotes cysteine http://purl.obolibrary.org/obo/CHEBI_15356
T387 1462-1469 Chemical denotes cystine http://purl.obolibrary.org/obo/CHEBI_17376
T388 1484-1497 Chemical denotes aspartic acid http://purl.obolibrary.org/obo/CHEBI_22660
T389 1493-1497 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T390 1506-1519 Chemical denotes glutamic acid http://purl.obolibrary.org/obo/CHEBI_16015|http://purl.obolibrary.org/obo/CHEBI_18237
T392 1515-1519 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T393 1531-1544 Chemical denotes phenylalanine http://purl.obolibrary.org/obo/CHEBI_28044|http://purl.obolibrary.org/obo/CHEBI_58095
T395 1559-1566 Chemical denotes glycine http://purl.obolibrary.org/obo/CHEBI_15428|http://purl.obolibrary.org/obo/CHEBI_29947|http://purl.obolibrary.org/obo/CHEBI_57305
T398 1578-1587 Chemical denotes histidine http://purl.obolibrary.org/obo/CHEBI_27570
T399 1599-1609 Chemical denotes isoleucine http://purl.obolibrary.org/obo/CHEBI_24898
T400 1621-1627 Chemical denotes lysine http://purl.obolibrary.org/obo/CHEBI_18019|http://purl.obolibrary.org/obo/CHEBI_25094
T402 1639-1646 Chemical denotes leucine http://purl.obolibrary.org/obo/CHEBI_25017
T403 1658-1668 Chemical denotes methionine http://purl.obolibrary.org/obo/CHEBI_16811|http://purl.obolibrary.org/obo/CHEBI_64558
T405 1683-1693 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T406 1708-1715 Chemical denotes proline http://purl.obolibrary.org/obo/CHEBI_17203|http://purl.obolibrary.org/obo/CHEBI_26271
T408 1724-1733 Chemical denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T409 1745-1753 Chemical denotes arginine http://purl.obolibrary.org/obo/CHEBI_16467|http://purl.obolibrary.org/obo/CHEBI_29016|http://purl.obolibrary.org/obo/CHEBI_32696
T412 1765-1771 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T413 1783-1792 Chemical denotes threonine http://purl.obolibrary.org/obo/CHEBI_26986
T414 1807-1813 Chemical denotes valine http://purl.obolibrary.org/obo/CHEBI_27266
T415 1828-1838 Chemical denotes tryptophan http://purl.obolibrary.org/obo/CHEBI_16828|http://purl.obolibrary.org/obo/CHEBI_27897|http://purl.obolibrary.org/obo/CHEBI_57719|http://purl.obolibrary.org/obo/CHEBI_57912
T419 1853-1861 Chemical denotes tyrosine http://purl.obolibrary.org/obo/CHEBI_18186

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T176 0-232 Sentence denotes Results and discussion in the present paper used the same amino acid codes as the above tools and data bank use, i.e. the IUPAC (International Union of Pure and Applied Chemistry) one letter amino acid codes, given in Table 1 below.
T177 233-310 Sentence denotes For completeness, conservative replacements in column 3 of Table 1 are given.
T178 311-416 Sentence denotes They relate largely to substitutions that can usefully be made in the design of synthetic peptides [4,5].
T179 417-671 Sentence denotes This is an application which is not specifically discussed in the present paper but which could be a basis for design of synthetic vaccines and preventative or therapeutic agents [4,5], in this case targeted at sialic acid glycan binding site of a virus.
T180 672-939 Sentence denotes As discussed in the sequence of steps for the methodology above, the sialic acid glycan binding motifs are taken to be indicators of the sialic acid binding domain and not necessarily of the target sites per se, but they may be, and often are, potential target sites.
T181 940-1142 Sentence denotes The list of conservative replacements also remains useful for considering substitutions that are conservative in maintaining similar amino acid properties when detecting and comparing related sequences.
T182 1143-1246 Sentence denotes Table 1 One letter amino acid codes and sialic acid site binding region measures discussed in the text.
T183 1247-1425 Sentence denotes One letter code Amino acid Conservative replacements Preliminary sialic acid binding amino acid score SABS (see Results) SABR-P prediction method refined parameters (see Results)
T184 1426-1450 Sentence denotes A alanine A, E, S, T 1 1
T185 1451-1481 Sentence denotes C cysteine/cystine S, T, V 1 1
T186 1482-1503 Sentence denotes D aspartic acid E 1 1
T187 1504-1528 Sentence denotes E glutamic acid A, D 0 0
T188 1529-1556 Sentence denotes F phenylalanine M, W, Y 1 2
T189 1557-1575 Sentence denotes G glycine N, P 1 1
T190 1576-1596 Sentence denotes H histidine K, R 1 2
T191 1597-1618 Sentence denotes I isoleucine L, V 0 0
T192 1619-1636 Sentence denotes K lysine H, R 0 0
T193 1637-1655 Sentence denotes L leucine I, V 0 0
T194 1656-1680 Sentence denotes M methionine F, W, Y 0 0
T195 1681-1705 Sentence denotes N asparagine G, D, Q 1 1
T196 1706-1721 Sentence denotes P proline G 0 0
T197 1722-1742 Sentence denotes Q glutamine N, E 0 0
T198 1743-1762 Sentence denotes R arginine H, K 0 0
T199 1763-1780 Sentence denotes S serine A, T 1 1
T200 1781-1804 Sentence denotes T threonine A, I, S 1 1
T201 1805-1825 Sentence denotes V valine A, I, L 0 0
T202 1826-1850 Sentence denotes W tryptophan F, M, Y 2 4
T203 1851-1864 Sentence denotes Y tyrosine F.
T204 1865-1873 Sentence denotes M, W 1 2

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
604 1737-1738 Gene denotes E Gene:43740570
605 1504-1505 Gene denotes E Gene:43740570
606 1498-1499 Gene denotes E Gene:43740570
607 1439-1440 Gene denotes E Gene:43740570
608 1734-1735 Gene denotes N Gene:43740575
609 1681-1682 Gene denotes N Gene:43740575
610 1567-1568 Gene denotes N Gene:43740575
611 1799-1800 Gene denotes S Gene:43740568
612 1763-1764 Gene denotes S Gene:43740568
613 1470-1471 Gene denotes S Gene:43740568
614 1442-1443 Gene denotes S Gene:43740568
615 1312-1323 Chemical denotes sialic acid MESH:D019158
616 1610-1611 Chemical denotes L MESH:D007930
617 1637-1638 Chemical denotes L MESH:D007930
618 1639-1646 Chemical denotes leucine MESH:D007930
619 1765-1771 Chemical denotes serine MESH:D012694
620 1820-1821 Chemical denotes L MESH:D007930
621 1451-1461 Disease denotes C cysteine MESH:C565659
623 1183-1194 Chemical denotes sialic acid MESH:D019158
629 103-107 Gene denotes bank Gene:55024
630 401-409 Chemical denotes peptides MESH:D010455
631 628-646 Chemical denotes sialic acid glycan
632 741-759 Chemical denotes sialic acid glycan
633 809-820 Chemical denotes sialic acid MESH:D019158