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PubMed:10704532 JSONTXT

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Glycan-Motif

Id Subject Object Predicate Lexical cue
T1 421-431 https://glytoucan.org/Structures/Glycans/G00017MO denotes hyaluronan
T2 476-487 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T3 598-609 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T4 648-659 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T5 709-719 https://glytoucan.org/Structures/Glycans/G00017MO denotes hyaluronan
T6 938-949 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T7 986-996 https://glytoucan.org/Structures/Glycans/G00017MO denotes hyaluronan
T8 1176-1197 https://glytoucan.org/Structures/Glycans/G34992DF denotes chondroitin-6-sulfate

GlyCosmos6-Glycan-Motif-Image

Id Subject Object Predicate Lexical cue image
T1 421-431 Glycan_Motif denotes hyaluronan https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00017MO
T2 476-487 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT
T3 598-609 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT
T4 648-659 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT
T5 709-719 Glycan_Motif denotes hyaluronan https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00017MO
T6 938-949 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT
T7 986-996 Glycan_Motif denotes hyaluronan https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00017MO
T8 1176-1197 Glycan_Motif denotes chondroitin-6-sulfate https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G34992DF
T9 1176-1187 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT

GlyCosmos6-Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 421-431 https://glytoucan.org/Structures/Glycans/G00017MO denotes hyaluronan
T2 476-487 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T3 598-609 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T4 648-659 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T5 709-719 https://glytoucan.org/Structures/Glycans/G00017MO denotes hyaluronan
T6 938-949 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T7 986-996 https://glytoucan.org/Structures/Glycans/G00017MO denotes hyaluronan
T8 1176-1197 https://glytoucan.org/Structures/Glycans/G34992DF denotes chondroitin-6-sulfate
T9 1176-1187 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin

Glycosmos6-MAT

Id Subject Object Predicate Lexical cue
T1 920-926 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T2 1027-1033 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T3 1253-1259 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T4 1328-1334 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T5 1613-1619 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed

sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-109 Sentence denotes Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?
TextSentencer_T2 110-274 Sentence denotes Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable.
TextSentencer_T3 275-432 Sentence denotes In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan.
TextSentencer_T4 433-631 Sentence denotes We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate.
TextSentencer_T5 632-777 Sentence denotes We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ.
TextSentencer_T6 778-1016 Sentence denotes This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold).
TextSentencer_T7 1017-1124 Sentence denotes Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations.
TextSentencer_T8 1125-1342 Sentence denotes Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix.
TextSentencer_T9 1343-1518 Sentence denotes Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns.
TextSentencer_T10 1519-1676 Sentence denotes Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds.
TextSentencer_T11 1677-1819 Sentence denotes However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement.
TextSentencer_T12 1820-1896 Sentence denotes Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.
T1 0-109 Sentence denotes Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?
T2 110-274 Sentence denotes Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable.
T3 275-432 Sentence denotes In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan.
T4 433-631 Sentence denotes We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate.
T5 632-777 Sentence denotes We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ.
T6 778-1016 Sentence denotes This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold).
T7 1017-1124 Sentence denotes Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations.
T8 1125-1342 Sentence denotes Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix.
T9 1343-1518 Sentence denotes Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns.
T10 1519-1676 Sentence denotes Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds.
T11 1677-1819 Sentence denotes However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement.
T12 1820-1896 Sentence denotes Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.
T1 0-109 Sentence denotes Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?
T2 110-274 Sentence denotes Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable.
T3 275-432 Sentence denotes In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan.
T4 433-631 Sentence denotes We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate.
T5 632-777 Sentence denotes We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ.
T6 778-1016 Sentence denotes This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold).
T7 1017-1124 Sentence denotes Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations.
T8 1125-1342 Sentence denotes Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix.
T9 1343-1518 Sentence denotes Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns.
T10 1519-1676 Sentence denotes Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds.
T11 1677-1819 Sentence denotes However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement.
T12 1820-1896 Sentence denotes Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.

Glycosmos6-GlycoEpitope

Id Subject Object Predicate Lexical cue
T1 476-487 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
T2 598-609 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
T3 648-659 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
T4 938-949 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
T5 1176-1197 http://www.glycoepitope.jp/epitopes/EP0083 denotes chondroitin-6-sulfate
T6 1176-1187 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin

GlycoBiology-FMA

Id Subject Object Predicate Lexical cue
_T1 0-17 FMAID:63011 denotes Glycosaminoglycan
_T2 0-17 FMAID:167395 denotes Glycosaminoglycan
_T3 91-96 FMAID:62912 denotes fiber
_T4 91-96 FMAID:167233 denotes fiber
_T5 110-127 FMAID:63011 denotes Glycosaminoglycan
_T6 110-127 FMAID:167395 denotes Glycosaminoglycan
_T7 128-135 FMAID:165447 denotes protein
_T8 128-135 FMAID:67257 denotes protein
_T9 358-360 FMAID:179042 denotes MD
_T10 421-431 FMAID:167396 denotes hyaluronan
_T11 421-431 FMAID:63014 denotes hyaluronan
_T12 492-500 FMAID:67104 denotes dermatan
_T13 492-500 FMAID:165189 denotes dermatan
_T14 598-630 FMAID:82837 denotes chondroitin and dermatan sulfate
_T15 598-630 FMAID:196838 denotes chondroitin and dermatan sulfate
_T16 614-622 FMAID:165189 denotes dermatan
_T17 614-622 FMAID:67104 denotes dermatan
_T18 614-630 FMAID:165192 denotes dermatan sulfate
_T19 709-719 FMAID:167396 denotes hyaluronan
_T20 709-719 FMAID:63014 denotes hyaluronan
_T21 867-872 FMAID:74547 denotes axial
_T22 867-872 FMAID:179284 denotes axial
_T23 915-919 FMAID:30334 denotes left
_T24 915-919 FMAID:171164 denotes left
_T25 915-926 FMAID:9714 denotes left-handed
_T26 915-926 FMAID:97630 denotes left-handed
_T27 920-926 FMAID:9712 denotes handed
_T28 920-926 FMAID:97627 denotes handed
_T29 986-996 FMAID:167396 denotes hyaluronan
_T30 986-996 FMAID:63014 denotes hyaluronan
_T31 1021-1026 FMAID:171315 denotes right
_T32 1021-1026 FMAID:30333 denotes right
_T33 1021-1033 FMAID:9713 denotes right-handed
_T34 1021-1033 FMAID:97629 denotes right-handed
_T35 1027-1033 FMAID:97627 denotes handed
_T36 1027-1033 FMAID:9712 denotes handed
_T37 1109-1111 FMAID:179042 denotes MD
_T38 1158-1163 FMAID:161427 denotes helix
_T39 1158-1163 FMAID:60992 denotes helix
_T40 1176-1197 FMAID:82837 denotes chondroitin-6-sulfate
_T41 1176-1197 FMAID:196838 denotes chondroitin-6-sulfate
_T42 1240-1245 FMAID:60992 denotes helix
_T43 1240-1245 FMAID:161427 denotes helix
_T44 1247-1252 FMAID:171315 denotes right
_T45 1247-1252 FMAID:30333 denotes right
_T46 1247-1259 FMAID:9713 denotes right-handed
_T47 1247-1259 FMAID:97629 denotes right-handed
_T48 1253-1259 FMAID:9712 denotes handed
_T49 1253-1259 FMAID:97627 denotes handed
_T50 1323-1327 FMAID:30334 denotes left
_T51 1323-1327 FMAID:171164 denotes left
_T52 1323-1334 FMAID:9714 denotes left-handed
_T53 1323-1334 FMAID:97630 denotes left-handed
_T54 1323-1341 FMAID:60994 denotes left-handed) helix
_T55 1323-1341 FMAID:161437 denotes left-handed) helix
_T56 1328-1334 FMAID:9712 denotes handed
_T57 1328-1334 FMAID:97627 denotes handed
_T58 1336-1341 FMAID:161427 denotes helix
_T59 1336-1341 FMAID:60992 denotes helix
_T60 1476-1484 FMAID:67104 denotes dermatan
_T61 1476-1484 FMAID:165189 denotes dermatan
_T62 1491-1496 FMAID:167233 denotes fiber
_T63 1491-1496 FMAID:62912 denotes fiber
_T64 1544-1552 FMAID:67104 denotes dermatan
_T65 1544-1552 FMAID:165189 denotes dermatan
_T66 1544-1560 FMAID:165192 denotes dermatan sulfate
_T67 1607-1612 FMAID:171315 denotes right
_T68 1607-1612 FMAID:30333 denotes right
_T69 1607-1619 FMAID:97629 denotes right-handed
_T70 1607-1619 FMAID:9713 denotes right-handed
_T71 1613-1619 FMAID:97627 denotes handed
_T72 1613-1619 FMAID:9712 denotes handed
_T73 1686-1688 FMAID:179042 denotes MD
_T74 1777-1782 FMAID:161427 denotes helix
_T75 1777-1782 FMAID:60992 denotes helix
_T76 1837-1845 FMAID:165189 denotes dermatan
_T77 1837-1845 FMAID:67104 denotes dermatan
_T78 1837-1853 FMAID:165192 denotes dermatan sulfate
_T79 1871-1876 FMAID:161427 denotes helix
_T80 1871-1876 FMAID:60992 denotes helix

uniprot-human

Id Subject Object Predicate Lexical cue
T1 673-679 http://www.uniprot.org/uniprot/Q92988 denotes beta(1
T2 744-750 http://www.uniprot.org/uniprot/Q92988 denotes beta(1
T3 1176-1197 http://www.uniprot.org/uniprot/Q9UQE7 denotes chondroitin-6-sulfate
T4 1390-1393 http://www.uniprot.org/uniprot/Q9NQP4 denotes C(1
T5 1582-1585 http://www.uniprot.org/uniprot/Q9NQP4 denotes C(1

GlycoBiology-NCBITAXON

Id Subject Object Predicate Lexical cue
T1 586-594 http://purl.bioontology.org/ontology/NCBITAXON/353209 denotes relating
T2 673-677 http://purl.bioontology.org/ontology/NCBITAXON/158455 denotes beta
T3 673-677 http://purl.bioontology.org/ontology/NCBITAXON/3554 denotes beta
T4 744-748 http://purl.bioontology.org/ontology/NCBITAXON/158455 denotes beta
T5 744-748 http://purl.bioontology.org/ontology/NCBITAXON/3554 denotes beta
T6 927-934 http://purl.bioontology.org/ontology/NCBITAXON/53324 denotes helices
T7 1034-1041 http://purl.bioontology.org/ontology/NCBITAXON/53324 denotes helices
T8 1158-1163 http://purl.bioontology.org/ontology/NCBITAXON/6534 denotes helix
T9 1240-1245 http://purl.bioontology.org/ontology/NCBITAXON/6534 denotes helix
T10 1276-1281 http://purl.bioontology.org/ontology/NCBITAXON/617048 denotes never
T11 1336-1341 http://purl.bioontology.org/ontology/NCBITAXON/6534 denotes helix
T12 1620-1627 http://purl.bioontology.org/ontology/NCBITAXON/53324 denotes helices
T13 1777-1782 http://purl.bioontology.org/ontology/NCBITAXON/6534 denotes helix
T14 1871-1876 http://purl.bioontology.org/ontology/NCBITAXON/6534 denotes helix

GO-BP

Id Subject Object Predicate Lexical cue
T1 623-630 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfate
T2 1190-1197 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfate
T3 1553-1560 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfate
T4 1846-1853 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfate

UBERON-AE

Id Subject Object Predicate Lexical cue
T1 1158-1163 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
T2 1240-1245 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
T3 1336-1341 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
T4 1777-1782 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
T5 1871-1876 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix

EDAM-topics

Id Subject Object Predicate Lexical cue
T1 43-61 http://edamontology.org/topic_0176 denotes molecular dynamics
T2 85-108 http://edamontology.org/topic_2828 denotes x-ray fiber diffraction
T3 128-135 http://edamontology.org/topic_0078 denotes protein
T4 128-148 http://edamontology.org/topic_3514 denotes protein interactions
T5 128-148 http://edamontology.org/topic_0130 denotes protein interactions
T6 128-148 http://edamontology.org/topic_0144 denotes protein interactions
T7 128-148 http://edamontology.org/topic_0148 denotes protein interactions
T8 128-148 http://edamontology.org/topic_0128 denotes protein interactions
T9 128-148 http://edamontology.org/topic_3515 denotes protein interactions
T10 128-148 http://edamontology.org/topic_0147 denotes protein interactions
T11 128-148 http://edamontology.org/topic_3526 denotes protein interactions
T12 136-148 http://edamontology.org/topic_0602 denotes interactions
T13 287-294 http://edamontology.org/topic_3678 denotes studies
T14 338-356 http://edamontology.org/topic_0176 denotes molecular dynamics
T15 388-405 http://edamontology.org/topic_2828 denotes x-ray diffraction
T16 557-574 http://edamontology.org/topic_2828 denotes x-ray diffraction
T17 685-692 http://edamontology.org/topic_0102 denotes linkage
T18 839-846 http://edamontology.org/topic_0102 denotes linkage
T19 903-911 http://edamontology.org/topic_3277 denotes sampling
T20 1090-1097 http://edamontology.org/topic_3277 denotes sampled
T21 1343-1361 http://edamontology.org/topic_0176 denotes Molecular dynamics
T22 1485-1508 http://edamontology.org/topic_2828 denotes x-ray fiber diffraction

EDAM-DFO

Id Subject Object Predicate Lexical cue
T1 43-73 http://edamontology.org/operation_2476 denotes molecular dynamics simulations
T2 128-135 http://edamontology.org/data_1467 denotes protein
T3 128-135 http://edamontology.org/format_1208 denotes protein
T4 128-148 http://edamontology.org/operation_2492 denotes protein interactions
T5 128-148 http://edamontology.org/data_0906 denotes protein interactions
T6 128-148 http://edamontology.org/data_1074 denotes protein interactions
T7 128-148 http://edamontology.org/data_2378 denotes protein interactions
T8 128-148 http://edamontology.org/data_1550 denotes protein interactions
T9 128-148 http://edamontology.org/format_2054 denotes protein interactions
T10 128-152 http://edamontology.org/operation_2949 denotes protein interactions are
T11 338-373 http://edamontology.org/operation_2476 denotes molecular dynamics (MD) simulations
T12 635-642 http://edamontology.org/operation_2423 denotes predict
T13 807-826 http://edamontology.org/data_1549 denotes in hydrogen-bonding
T14 1343-1373 http://edamontology.org/operation_2476 denotes Molecular dynamics simulations
T15 1701-1708 http://edamontology.org/operation_2423 denotes predict
T16 1793-1803 http://edamontology.org/data_0883 denotes structures
T17 1793-1807 http://edamontology.org/operation_1848 denotes structures for
T18 1890-1895 http://edamontology.org/data_2192 denotes error

GlycoBiology-MAT

Id Subject Object Predicate Lexical cue
T1 920-926 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T2 1027-1033 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T3 1253-1259 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T4 1328-1334 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed
T5 1613-1619 http://purl.obolibrary.org/obo/MAT_0000091 denotes handed

GlycoBiology-Motifs

Id Subject Object Predicate Lexical cue
T1 476-487 http://rdf.glycoinfo.org/glycan/G00018MO denotes chondroitin
T2 598-609 http://rdf.glycoinfo.org/glycan/G00018MO denotes chondroitin
T3 648-659 http://rdf.glycoinfo.org/glycan/G00018MO denotes chondroitin
T4 938-949 http://rdf.glycoinfo.org/glycan/G00018MO denotes chondroitin
T5 1176-1187 http://rdf.glycoinfo.org/glycan/G00018MO denotes chondroitin
T6 614-630 http://rdf.glycoinfo.org/glycan/G00019MO denotes dermatan sulfate
T7 1544-1560 http://rdf.glycoinfo.org/glycan/G00019MO denotes dermatan sulfate
T8 1837-1853 http://rdf.glycoinfo.org/glycan/G00019MO denotes dermatan sulfate

GlycoBiology-Epitope

Id Subject Object Predicate Lexical cue
PD-GlycoEpitope-B_T1 476-487 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
PD-GlycoEpitope-B_T2 598-609 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
PD-GlycoEpitope-B_T3 648-659 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
PD-GlycoEpitope-B_T4 938-949 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
PD-GlycoEpitope-B_T5 1176-1187 http://www.glycoepitope.jp/epitopes/EP0081 denotes chondroitin
PD-GlycoEpitope-B_T6 1176-1197 http://www.glycoepitope.jp/epitopes/EP0083 denotes chondroitin-6-sulfate

performance-test

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 1158-1163 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
PD-UBERON-AE-B_T2 1240-1245 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
PD-UBERON-AE-B_T3 1336-1341 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
PD-UBERON-AE-B_T4 1777-1782 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
PD-UBERON-AE-B_T5 1871-1876 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix

GlyCosmos15-Glycan

Id Subject Object Predicate Lexical cue image
T1 476-487 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T2 598-609 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T3 648-659 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T4 938-949 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T5 1176-1197 Glycan denotes chondroitin-6-sulfate https://api.glycosmos.org/wurcs2image/latest/png/binary/G34992DF

Anatomy-MAT

Id Subject Object Predicate Lexical cue mat_id
T1 920-926 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T2 1027-1033 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T3 1253-1259 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T4 1328-1334 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T5 1613-1619 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091

Glycan-GlyCosmos

Id Subject Object Predicate Lexical cue image
T1 476-487 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T2 598-609 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T3 648-659 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T4 938-949 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T5 1176-1197 Glycan denotes chondroitin-6-sulfate https://api.glycosmos.org/wurcs2image/latest/png/binary/G34992DF

GlyCosmos15-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1158-1163 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T2 1240-1245 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T3 1336-1341 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T4 1777-1782 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T5 1871-1876 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488

GlyCosmos15-Sentences

Id Subject Object Predicate Lexical cue
T1 0-109 Sentence denotes Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?
T2 110-274 Sentence denotes Glycosaminoglycan-protein interactions are biologically important and require an appreciation of glycan molecular shape in solution, which is presently unavailable.
T3 275-432 Sentence denotes In previous studies we found strong similarity between aqueous molecular dynamics (MD) simulations and published x-ray diffraction refinements of hyaluronan.
T4 433-631 Sentence denotes We have applied a similar approach here to chondroitin and dermatan, attempting to clarify some of the issues raised by the x-ray diffraction literature relating to chondroitin and dermatan sulfate.
T5 632-777 Sentence denotes We predict that chondroitin has the same beta(1-->4) linkage conformation as hyaluronan, and that their average beta(1-->3) conformations differ.
T6 778-1016 Sentence denotes This is explained by changes in hydrogen-bonding across this linkage, resulting from its axial hydroxyl, causing a different sampling of left-handed helices in chondroitin (2.5- to 3.5-fold) as compared with hyaluronan (3.0- to 4.0-fold).
T7 1017-1124 Sentence denotes Few right-handed helices, which lack intramolecular hydrogen-bonds, were sampled during our MD simulations.
T8 1125-1342 Sentence denotes Thus, we propose that the 8-fold helix observed in chondroitin-6-sulfate, represented in the literature as an 8(3) helix (right-handed), though it has never been refined, is more likely to be 8(5) (left-handed) helix.
T9 1343-1518 Sentence denotes Molecular dynamics simulations implied that (4)C(1) and (2)S(O), but not (1)C(4), forms of iduronate could be used in refinements of dermatan x-ray fiber diffraction patterns.
T10 1519-1676 Sentence denotes Current models of 8-fold dermatan sulfate chains containing (4)C(1) iduronate refine to right-handed helices, which possess no intramolecular hydrogen-bonds.
T11 1677-1819 Sentence denotes However, MD simulations predict that models containing (2)S(O) iduronate could provide better (8(5) helix) starting structures for refinement.
T12 1820-1896 Sentence denotes Thus, the 8-fold dermatan sulfate refinement (8(3) helix) could be in error.

GlyCosmos15-GlycoEpitope

Id Subject Object Predicate Lexical cue glycoepitope_id
T1 476-487 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T2 598-609 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T3 648-659 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T4 938-949 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T5 1176-1197 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin-6-sulfate http://www.glycoepitope.jp/epitopes/EP0083

GlyCosmos15-FMA

Id Subject Object Predicate Lexical cue db_id
T1 915-926 Body_part denotes left-handed FMA:9714
T2 1021-1033 Body_part denotes right-handed FMA:9713
T3 1158-1163 Body_part denotes helix FMA:60992
T4 1240-1245 Body_part denotes helix FMA:60992
T5 1247-1259 Body_part denotes right-handed FMA:9713
T6 1323-1334 Body_part denotes left-handed FMA:9714
T7 1336-1341 Body_part denotes helix FMA:60992
T8 1607-1619 Body_part denotes right-handed FMA:9713
T9 1777-1782 Body_part denotes helix FMA:60992
T10 1871-1876 Body_part denotes helix FMA:60992

GlyCosmos15-MAT

Id Subject Object Predicate Lexical cue mat_id
T1 920-926 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T2 1027-1033 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T3 1253-1259 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T4 1328-1334 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091
T5 1613-1619 Body_part denotes handed http://purl.obolibrary.org/obo/MAT_0000091

GlyCosmos-GlycoEpitope

Id Subject Object Predicate Lexical cue glycoepitope_id
T1 476-487 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T2 598-609 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T3 648-659 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T4 938-949 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T5 1176-1197 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin-6-sulfate http://www.glycoepitope.jp/epitopes/EP0083

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1158-1163 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T2 1240-1245 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T3 1336-1341 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T4 1777-1782 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T5 1871-1876 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488