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LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T219","span":{"begin":76,"end":83},"obj":"Chemical"},{"id":"T220","span":{"begin":147,"end":160},"obj":"Chemical"},{"id":"T221","span":{"begin":233,"end":246},"obj":"Chemical"},{"id":"T222","span":{"begin":950,"end":963},"obj":"Chemical"},{"id":"T223","span":{"begin":1065,"end":1072},"obj":"Chemical"},{"id":"T224","span":{"begin":1098,"end":1106},"obj":"Chemical"}],"attributes":[{"id":"A219","pred":"chebi_id","subj":"T219","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A220","pred":"chebi_id","subj":"T220","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A221","pred":"chebi_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A222","pred":"chebi_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A223","pred":"chebi_id","subj":"T223","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A224","pred":"chebi_id","subj":"T224","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Our glycomics-informed glycoproteomics allowed us to assign defined sets of glycans to specific glycosylation sites on 3D-structures of S and ACE2 glycoproteins based on experimental evidence (Figures 4 and 6). Similar to almost all glycoproteins, microheterogeneity is evident at most glycosylation sites of S and ACE2; each glycosylation site can be modified with one of several glycan structures, generating site-specific glycosylation portfolios. For modeling purposes, however, explicit structures must be placed at each glycosylation site. In order to capture the impact of microheterogeneity on S and ACE2 MD we chose to generate glycoforms for modeling that represented reasonable portfolios of glycan types. Using three glycoform models for S (Abundance, Oxford Class, and Processed) and two models for ACE2 (Abundance, which was equivalent to Oxford Class, and Processed), we generated three MD simulations of the co-complexes of these two glycoproteins (Figure 7; Videos S5, S6, and S7). The observed interactions over time allowed us to evaluate glycan-protein contacts between the two proteins and examine potential glycan-glycan interactions (Figure 7)."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T240","span":{"begin":0,"end":210},"obj":"Sentence"},{"id":"T241","span":{"begin":211,"end":450},"obj":"Sentence"},{"id":"T242","span":{"begin":451,"end":545},"obj":"Sentence"},{"id":"T243","span":{"begin":546,"end":716},"obj":"Sentence"},{"id":"T244","span":{"begin":717,"end":998},"obj":"Sentence"},{"id":"T245","span":{"begin":999,"end":1167},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Our glycomics-informed glycoproteomics allowed us to assign defined sets of glycans to specific glycosylation sites on 3D-structures of S and ACE2 glycoproteins based on experimental evidence (Figures 4 and 6). Similar to almost all glycoproteins, microheterogeneity is evident at most glycosylation sites of S and ACE2; each glycosylation site can be modified with one of several glycan structures, generating site-specific glycosylation portfolios. For modeling purposes, however, explicit structures must be placed at each glycosylation site. In order to capture the impact of microheterogeneity on S and ACE2 MD we chose to generate glycoforms for modeling that represented reasonable portfolios of glycan types. Using three glycoform models for S (Abundance, Oxford Class, and Processed) and two models for ACE2 (Abundance, which was equivalent to Oxford Class, and Processed), we generated three MD simulations of the co-complexes of these two glycoproteins (Figure 7; Videos S5, S6, and S7). The observed interactions over time allowed us to evaluate glycan-protein contacts between the two proteins and examine potential glycan-glycan interactions (Figure 7)."}

LitCovid-sample-UniProt

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T107","span":{"begin":110,"end":115},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T108","span":{"begin":300,"end":305},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T109","span":{"begin":340,"end":344},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T110","span":{"begin":411,"end":415},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T111","span":{"begin":540,"end":544},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"Our glycomics-informed glycoproteomics allowed us to assign defined sets of glycans to specific glycosylation sites on 3D-structures of S and ACE2 glycoproteins based on experimental evidence (Figures 4 and 6). Similar to almost all glycoproteins, microheterogeneity is evident at most glycosylation sites of S and ACE2; each glycosylation site can be modified with one of several glycan structures, generating site-specific glycosylation portfolios. For modeling purposes, however, explicit structures must be placed at each glycosylation site. In order to capture the impact of microheterogeneity on S and ACE2 MD we chose to generate glycoforms for modeling that represented reasonable portfolios of glycan types. Using three glycoform models for S (Abundance, Oxford Class, and Processed) and two models for ACE2 (Abundance, which was equivalent to Oxford Class, and Processed), we generated three MD simulations of the co-complexes of these two glycoproteins (Figure 7; Videos S5, S6, and S7). The observed interactions over time allowed us to evaluate glycan-protein contacts between the two proteins and examine potential glycan-glycan interactions (Figure 7)."}

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T115","span":{"begin":147,"end":160},"obj":"Body_part"},{"id":"T116","span":{"begin":233,"end":246},"obj":"Body_part"},{"id":"T117","span":{"begin":950,"end":963},"obj":"Body_part"},{"id":"T118","span":{"begin":1065,"end":1072},"obj":"Body_part"},{"id":"T119","span":{"begin":1098,"end":1106},"obj":"Body_part"}],"attributes":[{"id":"A115","pred":"fma_id","subj":"T115","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A116","pred":"fma_id","subj":"T116","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Our glycomics-informed glycoproteomics allowed us to assign defined sets of glycans to specific glycosylation sites on 3D-structures of S and ACE2 glycoproteins based on experimental evidence (Figures 4 and 6). Similar to almost all glycoproteins, microheterogeneity is evident at most glycosylation sites of S and ACE2; each glycosylation site can be modified with one of several glycan structures, generating site-specific glycosylation portfolios. For modeling purposes, however, explicit structures must be placed at each glycosylation site. In order to capture the impact of microheterogeneity on S and ACE2 MD we chose to generate glycoforms for modeling that represented reasonable portfolios of glycan types. Using three glycoform models for S (Abundance, Oxford Class, and Processed) and two models for ACE2 (Abundance, which was equivalent to Oxford Class, and Processed), we generated three MD simulations of the co-complexes of these two glycoproteins (Figure 7; Videos S5, S6, and S7). The observed interactions over time allowed us to evaluate glycan-protein contacts between the two proteins and examine potential glycan-glycan interactions (Figure 7)."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T89","span":{"begin":96,"end":109},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T90","span":{"begin":286,"end":299},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T91","span":{"begin":326,"end":339},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T92","span":{"begin":425,"end":438},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T93","span":{"begin":526,"end":539},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Our glycomics-informed glycoproteomics allowed us to assign defined sets of glycans to specific glycosylation sites on 3D-structures of S and ACE2 glycoproteins based on experimental evidence (Figures 4 and 6). Similar to almost all glycoproteins, microheterogeneity is evident at most glycosylation sites of S and ACE2; each glycosylation site can be modified with one of several glycan structures, generating site-specific glycosylation portfolios. For modeling purposes, however, explicit structures must be placed at each glycosylation site. In order to capture the impact of microheterogeneity on S and ACE2 MD we chose to generate glycoforms for modeling that represented reasonable portfolios of glycan types. Using three glycoform models for S (Abundance, Oxford Class, and Processed) and two models for ACE2 (Abundance, which was equivalent to Oxford Class, and Processed), we generated three MD simulations of the co-complexes of these two glycoproteins (Figure 7; Videos S5, S6, and S7). The observed interactions over time allowed us to evaluate glycan-protein contacts between the two proteins and examine potential glycan-glycan interactions (Figure 7)."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T85","span":{"begin":96,"end":109},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T86","span":{"begin":286,"end":299},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T87","span":{"begin":326,"end":339},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T88","span":{"begin":425,"end":438},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T89","span":{"begin":526,"end":539},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Our glycomics-informed glycoproteomics allowed us to assign defined sets of glycans to specific glycosylation sites on 3D-structures of S and ACE2 glycoproteins based on experimental evidence (Figures 4 and 6). Similar to almost all glycoproteins, microheterogeneity is evident at most glycosylation sites of S and ACE2; each glycosylation site can be modified with one of several glycan structures, generating site-specific glycosylation portfolios. For modeling purposes, however, explicit structures must be placed at each glycosylation site. In order to capture the impact of microheterogeneity on S and ACE2 MD we chose to generate glycoforms for modeling that represented reasonable portfolios of glycan types. Using three glycoform models for S (Abundance, Oxford Class, and Processed) and two models for ACE2 (Abundance, which was equivalent to Oxford Class, and Processed), we generated three MD simulations of the co-complexes of these two glycoproteins (Figure 7; Videos S5, S6, and S7). The observed interactions over time allowed us to evaluate glycan-protein contacts between the two proteins and examine potential glycan-glycan interactions (Figure 7)."}