PMC:7219429 / 19464-19838
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7219429","sourcedb":"PMC","sourceid":"7219429","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7219429","text":"MD simulations of GM1-spike protein interaction in a lipid raft domain. Two GM1 gangliosides were merged with eight cholesterol (chol) and two sphingomyelin (SM) lipids. After initial docking, MD simulations were performed for 50 ns. Two distinct views of the complex are shown. Cholesterol and sphingomyelin stabilize a dimer of GM1 clamped by the NTD of the spike protein.","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T112","span":{"begin":28,"end":35},"obj":"Body_part"},{"id":"T113","span":{"begin":53,"end":58},"obj":"Body_part"},{"id":"T114","span":{"begin":80,"end":92},"obj":"Body_part"},{"id":"T115","span":{"begin":366,"end":373},"obj":"Body_part"}],"attributes":[{"id":"A112","pred":"fma_id","subj":"T112","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A113","pred":"fma_id","subj":"T113","obj":"http://purl.org/sig/ont/fma/fma67264"},{"id":"A114","pred":"fma_id","subj":"T114","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A115","pred":"fma_id","subj":"T115","obj":"http://purl.org/sig/ont/fma/fma67257"},{"subj":"T112","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T113","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T114","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T115","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T72","span":{"begin":349,"end":352},"obj":"Disease"}],"attributes":[{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A73","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T193","span":{"begin":0,"end":2},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T194","span":{"begin":51,"end":52},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T195","span":{"begin":193,"end":195},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T196","span":{"begin":319,"end":320},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T193","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T194","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T195","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T196","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T344","span":{"begin":0,"end":2},"obj":"Chemical"},{"id":"T345","span":{"begin":18,"end":21},"obj":"Chemical"},{"id":"T348","span":{"begin":28,"end":35},"obj":"Chemical"},{"id":"T349","span":{"begin":53,"end":58},"obj":"Chemical"},{"id":"T350","span":{"begin":76,"end":79},"obj":"Chemical"},{"id":"T353","span":{"begin":80,"end":92},"obj":"Chemical"},{"id":"T354","span":{"begin":116,"end":127},"obj":"Chemical"},{"id":"T355","span":{"begin":129,"end":133},"obj":"Chemical"},{"id":"T356","span":{"begin":143,"end":156},"obj":"Chemical"},{"id":"T358","span":{"begin":158,"end":160},"obj":"Chemical"},{"id":"T361","span":{"begin":162,"end":168},"obj":"Chemical"},{"id":"T362","span":{"begin":193,"end":195},"obj":"Chemical"},{"id":"T363","span":{"begin":279,"end":290},"obj":"Chemical"},{"id":"T364","span":{"begin":295,"end":308},"obj":"Chemical"},{"id":"T366","span":{"begin":330,"end":333},"obj":"Chemical"},{"id":"T369","span":{"begin":366,"end":373},"obj":"Chemical"}],"attributes":[{"id":"A344","pred":"chebi_id","subj":"T344","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A345","pred":"chebi_id","subj":"T345","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A346","pred":"chebi_id","subj":"T345","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A347","pred":"chebi_id","subj":"T345","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A348","pred":"chebi_id","subj":"T348","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A349","pred":"chebi_id","subj":"T349","obj":"http://purl.obolibrary.org/obo/CHEBI_18059"},{"id":"A350","pred":"chebi_id","subj":"T350","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A351","pred":"chebi_id","subj":"T350","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A352","pred":"chebi_id","subj":"T350","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A353","pred":"chebi_id","subj":"T353","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A354","pred":"chebi_id","subj":"T354","obj":"http://purl.obolibrary.org/obo/CHEBI_16113"},{"id":"A355","pred":"chebi_id","subj":"T355","obj":"http://purl.obolibrary.org/obo/CHEBI_16113"},{"id":"A356","pred":"chebi_id","subj":"T356","obj":"http://purl.obolibrary.org/obo/CHEBI_17636"},{"id":"A357","pred":"chebi_id","subj":"T356","obj":"http://purl.obolibrary.org/obo/CHEBI_64583"},{"id":"A358","pred":"chebi_id","subj":"T358","obj":"http://purl.obolibrary.org/obo/CHEBI_17076"},{"id":"A359","pred":"chebi_id","subj":"T358","obj":"http://purl.obolibrary.org/obo/CHEBI_74817"},{"id":"A360","pred":"chebi_id","subj":"T358","obj":"http://purl.obolibrary.org/obo/CHEBI_17636"},{"id":"A361","pred":"chebi_id","subj":"T361","obj":"http://purl.obolibrary.org/obo/CHEBI_18059"},{"id":"A362","pred":"chebi_id","subj":"T362","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A363","pred":"chebi_id","subj":"T363","obj":"http://purl.obolibrary.org/obo/CHEBI_16113"},{"id":"A364","pred":"chebi_id","subj":"T364","obj":"http://purl.obolibrary.org/obo/CHEBI_17636"},{"id":"A365","pred":"chebi_id","subj":"T364","obj":"http://purl.obolibrary.org/obo/CHEBI_64583"},{"id":"A366","pred":"chebi_id","subj":"T366","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A367","pred":"chebi_id","subj":"T366","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A368","pred":"chebi_id","subj":"T366","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A369","pred":"chebi_id","subj":"T369","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"subj":"T344","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T345","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T348","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T349","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T350","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T353","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T354","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T355","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T356","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T358","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T361","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T362","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T363","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T364","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T366","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T369","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T21","span":{"begin":18,"end":21},"obj":"GlycoEpitope"},{"id":"T22","span":{"begin":76,"end":79},"obj":"GlycoEpitope"},{"id":"T23","span":{"begin":330,"end":333},"obj":"GlycoEpitope"}],"attributes":[{"id":"A21","pred":"glyco_epitope_db_id","subj":"T21","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A22","pred":"glyco_epitope_db_id","subj":"T22","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A23","pred":"glyco_epitope_db_id","subj":"T23","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"subj":"T21","pred":"source","obj":"LitCovid-PD-GlycoEpitope"},{"subj":"T22","pred":"source","obj":"LitCovid-PD-GlycoEpitope"},{"subj":"T23","pred":"source","obj":"LitCovid-PD-GlycoEpitope"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T144","span":{"begin":72,"end":169},"obj":"Sentence"},{"id":"T145","span":{"begin":170,"end":233},"obj":"Sentence"},{"id":"T146","span":{"begin":234,"end":278},"obj":"Sentence"},{"id":"T147","span":{"begin":279,"end":374},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T144","pred":"source","obj":"LitCovid-sentences"},{"subj":"T145","pred":"source","obj":"LitCovid-sentences"},{"subj":"T146","pred":"source","obj":"LitCovid-sentences"},{"subj":"T147","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"457","span":{"begin":360,"end":365},"obj":"Gene"},{"id":"458","span":{"begin":18,"end":21},"obj":"Chemical"},{"id":"459","span":{"begin":53,"end":58},"obj":"Chemical"},{"id":"460","span":{"begin":76,"end":79},"obj":"Chemical"},{"id":"461","span":{"begin":80,"end":92},"obj":"Chemical"},{"id":"462","span":{"begin":116,"end":127},"obj":"Chemical"},{"id":"463","span":{"begin":129,"end":133},"obj":"Chemical"},{"id":"464","span":{"begin":143,"end":156},"obj":"Chemical"},{"id":"465","span":{"begin":158,"end":160},"obj":"Chemical"},{"id":"466","span":{"begin":162,"end":168},"obj":"Chemical"},{"id":"467","span":{"begin":279,"end":290},"obj":"Chemical"},{"id":"468","span":{"begin":295,"end":308},"obj":"Chemical"},{"id":"469","span":{"begin":330,"end":333},"obj":"Chemical"}],"attributes":[{"id":"A457","pred":"tao:has_database_id","subj":"457","obj":"Gene:43740568"},{"id":"A458","pred":"tao:has_database_id","subj":"458","obj":"MESH:D005677"},{"id":"A459","pred":"tao:has_database_id","subj":"459","obj":"MESH:D008055"},{"id":"A460","pred":"tao:has_database_id","subj":"460","obj":"MESH:D005677"},{"id":"A461","pred":"tao:has_database_id","subj":"461","obj":"MESH:D005732"},{"id":"A462","pred":"tao:has_database_id","subj":"462","obj":"MESH:D002784"},{"id":"A463","pred":"tao:has_database_id","subj":"463","obj":"MESH:D002784"},{"id":"A464","pred":"tao:has_database_id","subj":"464","obj":"MESH:D013109"},{"id":"A465","pred":"tao:has_database_id","subj":"465","obj":"MESH:D013109"},{"id":"A466","pred":"tao:has_database_id","subj":"466","obj":"MESH:D008055"},{"id":"A467","pred":"tao:has_database_id","subj":"467","obj":"MESH:D002784"},{"id":"A468","pred":"tao:has_database_id","subj":"468","obj":"MESH:D013109"},{"id":"A469","pred":"tao:has_database_id","subj":"469","obj":"MESH:D005677"},{"subj":"457","pred":"source","obj":"LitCovid-PubTator"},{"subj":"458","pred":"source","obj":"LitCovid-PubTator"},{"subj":"459","pred":"source","obj":"LitCovid-PubTator"},{"subj":"460","pred":"source","obj":"LitCovid-PubTator"},{"subj":"461","pred":"source","obj":"LitCovid-PubTator"},{"subj":"462","pred":"source","obj":"LitCovid-PubTator"},{"subj":"463","pred":"source","obj":"LitCovid-PubTator"},{"subj":"464","pred":"source","obj":"LitCovid-PubTator"},{"subj":"465","pred":"source","obj":"LitCovid-PubTator"},{"subj":"466","pred":"source","obj":"LitCovid-PubTator"},{"subj":"467","pred":"source","obj":"LitCovid-PubTator"},{"subj":"468","pred":"source","obj":"LitCovid-PubTator"},{"subj":"469","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#93bfec","default":true},{"id":"LitCovid-PD-MONDO","color":"#d9ec93"},{"id":"LitCovid-PD-CLO","color":"#e593ec"},{"id":"LitCovid-PD-CHEBI","color":"#93eccb"},{"id":"LitCovid-PD-GlycoEpitope","color":"#ecb193"},{"id":"LitCovid-sentences","color":"#9793ec"},{"id":"LitCovid-PubTator","color":"#a9ec93"}]}]}}