PMC:7219429 / 25156-26385 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T156","span":{"begin":277,"end":284},"obj":"Body_part"},{"id":"T157","span":{"begin":423,"end":430},"obj":"Body_part"},{"id":"T158","span":{"begin":431,"end":442},"obj":"Body_part"},{"id":"T159","span":{"begin":551,"end":562},"obj":"Body_part"},{"id":"T160","span":{"begin":655,"end":667},"obj":"Body_part"},{"id":"T161","span":{"begin":845,"end":861},"obj":"Body_part"},{"id":"T162","span":{"begin":908,"end":920},"obj":"Body_part"},{"id":"T163","span":{"begin":1009,"end":1021},"obj":"Body_part"},{"id":"T164","span":{"begin":1134,"end":1146},"obj":"Body_part"},{"id":"T165","span":{"begin":1206,"end":1211},"obj":"Body_part"}],"attributes":[{"id":"A156","pred":"fma_id","subj":"T156","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A157","pred":"fma_id","subj":"T157","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A158","pred":"fma_id","subj":"T158","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A159","pred":"fma_id","subj":"T159","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A160","pred":"fma_id","subj":"T160","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A161","pred":"fma_id","subj":"T161","obj":"http://purl.org/sig/ont/fma/fma82742"},{"id":"A162","pred":"fma_id","subj":"T162","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A163","pred":"fma_id","subj":"T163","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A164","pred":"fma_id","subj":"T164","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A165","pred":"fma_id","subj":"T165","obj":"http://purl.org/sig/ont/fma/fma67264"}],"text":"In this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T237","span":{"begin":72,"end":77},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T238","span":{"begin":211,"end":212},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T239","span":{"begin":259,"end":261},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T240","span":{"begin":579,"end":587},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T241","span":{"begin":668,"end":671},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T242","span":{"begin":672,"end":673},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T243","span":{"begin":1025,"end":1033},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T244","span":{"begin":1075,"end":1077},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T245","span":{"begin":1204,"end":1205},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"In this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":72,"end":95},"obj":"http://purl.obolibrary.org/obo/GO_0019048"}],"text":"In this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T186","span":{"begin":0,"end":184},"obj":"Sentence"},{"id":"T187","span":{"begin":185,"end":349},"obj":"Sentence"},{"id":"T188","span":{"begin":350,"end":616},"obj":"Sentence"},{"id":"T189","span":{"begin":617,"end":814},"obj":"Sentence"},{"id":"T190","span":{"begin":815,"end":921},"obj":"Sentence"},{"id":"T191","span":{"begin":922,"end":1070},"obj":"Sentence"},{"id":"T192","span":{"begin":1071,"end":1229},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"696","span":{"begin":162,"end":168},"obj":"Chemical"},{"id":"697","span":{"begin":431,"end":442},"obj":"Chemical"},{"id":"698","span":{"begin":514,"end":519},"obj":"Chemical"},{"id":"699","span":{"begin":528,"end":538},"obj":"Chemical"},{"id":"700","span":{"begin":551,"end":562},"obj":"Chemical"},{"id":"701","span":{"begin":597,"end":605},"obj":"Chemical"},{"id":"702","span":{"begin":636,"end":644},"obj":"Chemical"},{"id":"703","span":{"begin":655,"end":667},"obj":"Chemical"},{"id":"704","span":{"begin":695,"end":705},"obj":"Chemical"},{"id":"705","span":{"begin":845,"end":861},"obj":"Chemical"},{"id":"706","span":{"begin":908,"end":920},"obj":"Chemical"},{"id":"707","span":{"begin":1009,"end":1021},"obj":"Chemical"},{"id":"708","span":{"begin":1134,"end":1146},"obj":"Chemical"},{"id":"709","span":{"begin":1161,"end":1172},"obj":"Chemical"},{"id":"710","span":{"begin":1177,"end":1190},"obj":"Chemical"},{"id":"711","span":{"begin":1206,"end":1211},"obj":"Chemical"}],"attributes":[{"id":"A697","pred":"tao:has_database_id","subj":"697","obj":"MESH:D005732"},{"id":"A698","pred":"tao:has_database_id","subj":"698","obj":"MESH:D014867"},{"id":"A699","pred":"tao:has_database_id","subj":"699","obj":"MESH:D002241"},{"id":"A700","pred":"tao:has_database_id","subj":"700","obj":"MESH:D005732"},{"id":"A701","pred":"tao:has_database_id","subj":"701","obj":"MESH:D002518"},{"id":"A702","pred":"tao:has_database_id","subj":"702","obj":"MESH:D002518"},{"id":"A703","pred":"tao:has_database_id","subj":"703","obj":"MESH:D005732"},{"id":"A704","pred":"tao:has_database_id","subj":"704","obj":"MESH:D002241"},{"id":"A705","pred":"tao:has_database_id","subj":"705","obj":"MESH:D009844"},{"id":"A706","pred":"tao:has_database_id","subj":"706","obj":"MESH:D005732"},{"id":"A707","pred":"tao:has_database_id","subj":"707","obj":"MESH:D005732"},{"id":"A708","pred":"tao:has_database_id","subj":"708","obj":"MESH:D005732"},{"id":"A709","pred":"tao:has_database_id","subj":"709","obj":"MESH:D002784"},{"id":"A710","pred":"tao:has_database_id","subj":"710","obj":"MESH:D013109"},{"id":"A711","pred":"tao:has_database_id","subj":"711","obj":"MESH:D008055"}],"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":"In this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment."}

2_test

{"project":"2_test","denotations":[{"id":"32405156-30236283-48151027","span":{"begin":345,"end":347},"obj":"30236283"},{"id":"32405156-23807078-48151028","span":{"begin":612,"end":614},"obj":"23807078"},{"id":"32405156-23772214-48151029","span":{"begin":810,"end":812},"obj":"23772214"},{"id":"32405156-31431523-48151030","span":{"begin":1060,"end":1062},"obj":"31431523"},{"id":"32405156-23772214-48151031","span":{"begin":1063,"end":1065},"obj":"23772214"},{"id":"32405156-27352802-48151032","span":{"begin":1066,"end":1068},"obj":"27352802"},{"id":"T72401","span":{"begin":345,"end":347},"obj":"30236283"},{"id":"T44542","span":{"begin":612,"end":614},"obj":"23807078"},{"id":"T20321","span":{"begin":810,"end":812},"obj":"23772214"},{"id":"T12506","span":{"begin":1060,"end":1062},"obj":"31431523"},{"id":"T69993","span":{"begin":1063,"end":1065},"obj":"23772214"},{"id":"T86224","span":{"begin":1066,"end":1068},"obj":"27352802"}],"text":"In this study, molecular modelling approaches specifically dedicated to virus-host interactions were used to unravel the antiviral mechanism of action of ATM and CLQ-OH in combination. The study method included a first round of molecular docking, followed by MD simulations of protein-ligand interactions to assess the robustness of each model [25]. Such computer-assisted simulations are particularly helpful for studying protein-ganglioside interactions as crystallographic approaches are usually limited to the water-soluble saccharide part of the ganglioside, neglecting the membrane embedded-ceramide part [31]. Unfortunately, the ceramide moiety of gangliosides has a marked effect on the saccharide part with which it interacts, resulting in significant restriction of its conformational possibilities [32]. Therefore, data obtained with oligosaccharides cannot be systematically transposed to intact gangliosides. Molecular modelling approaches circumvented this difficulty and enabled study of whole gangliosides in membrane-compatible conformations [16,32,33]. The MD simulations performed in the present study were done on gangliosides surrounded by cholesterol and sphingomyelin, which mimic a lipid raft environment."}