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LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T188","span":{"begin":393,"end":405},"obj":"Chemical"}],"attributes":[{"id":"A188","pred":"chebi_id","subj":"T188","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T82","span":{"begin":537,"end":542},"obj":"Species"},{"id":"T83","span":{"begin":815,"end":821},"obj":"Species"},{"id":"T84","span":{"begin":868,"end":873},"obj":"Species"},{"id":"T85","span":{"begin":1112,"end":1117},"obj":"Species"},{"id":"T86","span":{"begin":1293,"end":1298},"obj":"Species"},{"id":"T87","span":{"begin":1317,"end":1322},"obj":"Species"},{"id":"T88","span":{"begin":1542,"end":1547},"obj":"Species"}],"attributes":[{"id":"A88","pred":"ncbi_taxonomy_id","subj":"T88","obj":"NCBItxid:9606"},{"id":"A82","pred":"ncbi_taxonomy_id","subj":"T82","obj":"NCBItxid:9606"},{"id":"A83","pred":"ncbi_taxonomy_id","subj":"T83","obj":"NCBItxid:9605"},{"id":"A86","pred":"ncbi_taxonomy_id","subj":"T86","obj":"NCBItxid:9606"},{"id":"A84","pred":"ncbi_taxonomy_id","subj":"T84","obj":"NCBItxid:9606"},{"id":"A87","pred":"ncbi_taxonomy_id","subj":"T87","obj":"NCBItxid:9606"},{"id":"A85","pred":"ncbi_taxonomy_id","subj":"T85","obj":"NCBItxid:9606"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T183","span":{"begin":0,"end":93},"obj":"Sentence"},{"id":"T184","span":{"begin":94,"end":219},"obj":"Sentence"},{"id":"T185","span":{"begin":220,"end":369},"obj":"Sentence"},{"id":"T186","span":{"begin":370,"end":588},"obj":"Sentence"},{"id":"T187","span":{"begin":589,"end":709},"obj":"Sentence"},{"id":"T188","span":{"begin":710,"end":897},"obj":"Sentence"},{"id":"T189","span":{"begin":898,"end":967},"obj":"Sentence"},{"id":"T190","span":{"begin":968,"end":1055},"obj":"Sentence"},{"id":"T191","span":{"begin":1056,"end":1122},"obj":"Sentence"},{"id":"T192","span":{"begin":1123,"end":1304},"obj":"Sentence"},{"id":"T193","span":{"begin":1305,"end":1437},"obj":"Sentence"},{"id":"T194","span":{"begin":1438,"end":1529},"obj":"Sentence"},{"id":"T195","span":{"begin":1530,"end":1642},"obj":"Sentence"},{"id":"T196","span":{"begin":1643,"end":1652},"obj":"Sentence"},{"id":"T197","span":{"begin":1653,"end":1706},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T59","span":{"begin":248,"end":252},"obj":"Disease"}],"attributes":[{"id":"A59","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0010408"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-UniProt

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T91","span":{"begin":459,"end":463},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T92","span":{"begin":723,"end":727},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T93","span":{"begin":1509,"end":1513},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T98","span":{"begin":393,"end":405},"obj":"Body_part"}],"attributes":[{"id":"A98","pred":"fma_id","subj":"T98","obj":"http://purl.org/sig/ont/fma/fma62925"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T73","span":{"begin":67,"end":80},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T74","span":{"begin":740,"end":753},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T75","span":{"begin":1487,"end":1500},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T69","span":{"begin":67,"end":80},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T70","span":{"begin":740,"end":753},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T71","span":{"begin":1487,"end":1500},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

2_test

{"project":"2_test","denotations":[{"id":"32841605-32225176-19659520","span":{"begin":238,"end":242},"obj":"32225176"}],"text":"3D Structural Modeling of Glycosylated, Soluble, ACE2-Highlighting Glycosylation and Variants\nWe integrated our glycomics, glycoproteomics, and population variant analyses results with a 3D model of Ace 2 (based on PDB: 6M0J (Lan et al., 2020; see STAR Methods for details) to generate two versions of the soluble glycosylated ACE2 for visualization and MD simulations. We visualized the ACE2 glycoprotein with the Abundance glycoform model simulated at each site as well as highlighting the naturally occurring variants observed in the human population (Figure 6 A; Video S2; Table S11). Note, that the Abundance glycoform model and the Oxford Class glycoform model for ACE2 are identical (Tables S1 and S8). Notably, one site of N-linked glycosylation (N546) is predicted to not be present in three out of 10,000 humans based on naturally occurring variation in the human population (Table S11). We also modeled ACE2 using the Processed glycoform model (Figure 6B). In both models, the interaction domain with S is defined (Figures 6A and 6B; Video S2).\nFigure 6 3D Structural Modeling of Glycosylated Soluble Human ACE2\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated soluble human ACE2.\n(A) Soluble human ACE2 model from MD simulations displaying abundance glycoforms, interaction surface with S, and sequence variants. N546 variant is boxed that would remove N-linked glycosylation at that site (see Video S2).\n(B) Soluble human ACE2 model from MD simulations displaying processed glycoforms and interaction surface with S.\nVideo S2. Glycosylated ACE2 with Variants, Related to Figure 6A"}

PMC:7443692 / 30921-32627 JSONTXT

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PMC:7443692 / 30921-32627 JSON TXT