PMC:7219429 / 8560-9018 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T38","span":{"begin":27,"end":38},"obj":"Body_part"},{"id":"T39","span":{"begin":73,"end":83},"obj":"Body_part"},{"id":"T40","span":{"begin":134,"end":144},"obj":"Body_part"},{"id":"T41","span":{"begin":252,"end":263},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma82780"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma82780"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma82816"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T81","span":{"begin":285,"end":293},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T82","span":{"begin":331,"end":332},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T83","span":{"begin":426,"end":434},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T111","span":{"begin":27,"end":42},"obj":"Chemical"},{"id":"T113","span":{"begin":27,"end":38},"obj":"Chemical"},{"id":"T114","span":{"begin":39,"end":42},"obj":"Chemical"},{"id":"T115","span":{"begin":73,"end":83},"obj":"Chemical"},{"id":"T116","span":{"begin":134,"end":144},"obj":"Chemical"},{"id":"T117","span":{"begin":252,"end":263},"obj":"Chemical"},{"id":"T118","span":{"begin":383,"end":386},"obj":"Chemical"},{"id":"T121","span":{"begin":387,"end":395},"obj":"Chemical"},{"id":"T122","span":{"begin":444,"end":452},"obj":"Chemical"}],"attributes":[{"id":"A111","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A112","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A113","pred":"chebi_id","subj":"T113","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A114","pred":"chebi_id","subj":"T114","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A115","pred":"chebi_id","subj":"T115","obj":"http://purl.obolibrary.org/obo/CHEBI_33563"},{"id":"A116","pred":"chebi_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/CHEBI_33563"},{"id":"A117","pred":"chebi_id","subj":"T117","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A118","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A119","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A120","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A121","pred":"chebi_id","subj":"T121","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A122","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_17761"},{"id":"A123","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_52639"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":39,"end":42},"obj":"GlycoEpitope"},{"id":"T5","span":{"begin":383,"end":386},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A5","pred":"glyco_epitope_db_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}

{"project":"LitCovid-sentences","denotations":[{"id":"T66","span":{"begin":0,"end":458},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}

{"project":"LitCovid-PubTator","denotations":[{"id":"255","span":{"begin":27,"end":38},"obj":"Chemical"},{"id":"256","span":{"begin":39,"end":42},"obj":"Chemical"},{"id":"257","span":{"begin":252,"end":263},"obj":"Chemical"},{"id":"258","span":{"begin":383,"end":386},"obj":"Chemical"},{"id":"259","span":{"begin":444,"end":452},"obj":"Chemical"},{"id":"272","span":{"begin":204,"end":228},"obj":"Disease"}],"attributes":[{"id":"A255","pred":"tao:has_database_id","subj":"255","obj":"MESH:D005732"},{"id":"A256","pred":"tao:has_database_id","subj":"256","obj":"MESH:D005677"},{"id":"A257","pred":"tao:has_database_id","subj":"257","obj":"MESH:D005732"},{"id":"A258","pred":"tao:has_database_id","subj":"258","obj":"MESH:D005677"},{"id":"A259","pred":"tao:has_database_id","subj":"259","obj":"MESH:D002518"},{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"MESH:C563601"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}

{"project":"2_test","denotations":[{"id":"32405156-30525595-48151020","span":{"begin":93,"end":95},"obj":"30525595"},{"id":"T58286","span":{"begin":93,"end":95},"obj":"30525595"}],"text":"The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part."}