PMC:7258756 / 19752-21293 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"288","span":{"begin":391,"end":396},"obj":"Gene"},{"id":"289","span":{"begin":327,"end":332},"obj":"Gene"},{"id":"290","span":{"begin":265,"end":270},"obj":"Gene"},{"id":"291","span":{"begin":34,"end":39},"obj":"Gene"},{"id":"292","span":{"begin":62,"end":72},"obj":"Species"},{"id":"293","span":{"begin":254,"end":264},"obj":"Species"},{"id":"294","span":{"begin":316,"end":326},"obj":"Species"},{"id":"295","span":{"begin":1163,"end":1171},"obj":"Species"}],"attributes":[{"id":"A288","pred":"tao:has_database_id","subj":"288","obj":"Gene:43740568"},{"id":"A289","pred":"tao:has_database_id","subj":"289","obj":"Gene:43740568"},{"id":"A290","pred":"tao:has_database_id","subj":"290","obj":"Gene:43740568"},{"id":"A291","pred":"tao:has_database_id","subj":"291","obj":"Gene:43740568"},{"id":"A292","pred":"tao:has_database_id","subj":"292","obj":"Tax:2697049"},{"id":"A293","pred":"tao:has_database_id","subj":"293","obj":"Tax:2697049"},{"id":"A294","pred":"tao:has_database_id","subj":"294","obj":"Tax:2697049"},{"id":"A295","pred":"tao:has_database_id","subj":"295","obj":"Tax:694009"}],"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 discontinuous epitopes in the spike protein of the Indian SARS-CoV-2 were further identified using multiple methods, Ellipro and DiscoTope. Conformational epitopes based on these methods were mapped on the pre-fusion structure of the modelled Indian SARS-CoV-2 spike protein. The newly released structure of the SARS-CoV-2 spike protein was used as the template for modelling the Indian spike protein. Ramachandran plot statistics revealed 83.7 per cent of the residues to be in the core region, 14.4 per cent in the additionally allowed region and 0.5 per cent in the disallowed region. Four epitopes were predicted by Ellipro based on the PI threshold of 0.8 (Supplementary Table II (available from http:/ /www. ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm7.pdf)). The result from the DiscoTope is presented in Supplementary Table III (available from http://www.ijmr.org.in/articles/ 2020/151/2/ images/ IndianJMedRes_2020_151_2_200_281471_sm8.pdf). The mapped conformational epitopes are depicted in Figure 2. For the purpose of comparison, the Indian S protein sequence was also modelled using the pre-fusion structure of SARS-CoV-1 (6ACC.PDB; 87.29% identity), and the results for the conformational epitopes predicted are in Supplementary Table IV (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_28147 1_sm9.pdf and Supplementary Figure 2 (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm10.pdf)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T98","span":{"begin":40,"end":47},"obj":"Body_part"},{"id":"T99","span":{"begin":271,"end":278},"obj":"Body_part"},{"id":"T100","span":{"begin":333,"end":340},"obj":"Body_part"},{"id":"T101","span":{"begin":397,"end":404},"obj":"Body_part"},{"id":"T102","span":{"begin":1094,"end":1101},"obj":"Body_part"}],"attributes":[{"id":"A98","pred":"fma_id","subj":"T98","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A99","pred":"fma_id","subj":"T99","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A100","pred":"fma_id","subj":"T100","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A101","pred":"fma_id","subj":"T101","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A102","pred":"fma_id","subj":"T102","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"The discontinuous epitopes in the spike protein of the Indian SARS-CoV-2 were further identified using multiple methods, Ellipro and DiscoTope. Conformational epitopes based on these methods were mapped on the pre-fusion structure of the modelled Indian SARS-CoV-2 spike protein. The newly released structure of the SARS-CoV-2 spike protein was used as the template for modelling the Indian spike protein. Ramachandran plot statistics revealed 83.7 per cent of the residues to be in the core region, 14.4 per cent in the additionally allowed region and 0.5 per cent in the disallowed region. Four epitopes were predicted by Ellipro based on the PI threshold of 0.8 (Supplementary Table II (available from http:/ /www. ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm7.pdf)). The result from the DiscoTope is presented in Supplementary Table III (available from http://www.ijmr.org.in/articles/ 2020/151/2/ images/ IndianJMedRes_2020_151_2_200_281471_sm8.pdf). The mapped conformational epitopes are depicted in Figure 2. For the purpose of comparison, the Indian S protein sequence was also modelled using the pre-fusion structure of SARS-CoV-1 (6ACC.PDB; 87.29% identity), and the results for the conformational epitopes predicted are in Supplementary Table IV (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_28147 1_sm9.pdf and Supplementary Figure 2 (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm10.pdf)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T153","span":{"begin":62,"end":70},"obj":"Disease"},{"id":"T154","span":{"begin":62,"end":66},"obj":"Disease"},{"id":"T155","span":{"begin":254,"end":262},"obj":"Disease"},{"id":"T156","span":{"begin":254,"end":258},"obj":"Disease"},{"id":"T157","span":{"begin":316,"end":324},"obj":"Disease"},{"id":"T158","span":{"begin":316,"end":320},"obj":"Disease"},{"id":"T159","span":{"begin":1163,"end":1171},"obj":"Disease"},{"id":"T160","span":{"begin":1163,"end":1167},"obj":"Disease"}],"attributes":[{"id":"A153","pred":"mondo_id","subj":"T153","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A154","pred":"mondo_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A155","pred":"mondo_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A156","pred":"mondo_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A157","pred":"mondo_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A158","pred":"mondo_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A159","pred":"mondo_id","subj":"T159","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A160","pred":"mondo_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The discontinuous epitopes in the spike protein of the Indian SARS-CoV-2 were further identified using multiple methods, Ellipro and DiscoTope. Conformational epitopes based on these methods were mapped on the pre-fusion structure of the modelled Indian SARS-CoV-2 spike protein. The newly released structure of the SARS-CoV-2 spike protein was used as the template for modelling the Indian spike protein. Ramachandran plot statistics revealed 83.7 per cent of the residues to be in the core region, 14.4 per cent in the additionally allowed region and 0.5 per cent in the disallowed region. Four epitopes were predicted by Ellipro based on the PI threshold of 0.8 (Supplementary Table II (available from http:/ /www. ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm7.pdf)). The result from the DiscoTope is presented in Supplementary Table III (available from http://www.ijmr.org.in/articles/ 2020/151/2/ images/ IndianJMedRes_2020_151_2_200_281471_sm8.pdf). The mapped conformational epitopes are depicted in Figure 2. For the purpose of comparison, the Indian S protein sequence was also modelled using the pre-fusion structure of SARS-CoV-1 (6ACC.PDB; 87.29% identity), and the results for the conformational epitopes predicted are in Supplementary Table IV (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_28147 1_sm9.pdf and Supplementary Figure 2 (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm10.pdf)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T99","span":{"begin":40,"end":47},"obj":"Chemical"},{"id":"T100","span":{"begin":271,"end":278},"obj":"Chemical"},{"id":"T101","span":{"begin":333,"end":340},"obj":"Chemical"},{"id":"T102","span":{"begin":397,"end":404},"obj":"Chemical"},{"id":"T103","span":{"begin":645,"end":647},"obj":"Chemical"},{"id":"T107","span":{"begin":686,"end":688},"obj":"Chemical"},{"id":"T108","span":{"begin":1094,"end":1101},"obj":"Chemical"},{"id":"T109","span":{"begin":1288,"end":1290},"obj":"Chemical"}],"attributes":[{"id":"A99","pred":"chebi_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A100","pred":"chebi_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A101","pred":"chebi_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A102","pred":"chebi_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A103","pred":"chebi_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/CHEBI_28874"},{"id":"A104","pred":"chebi_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/CHEBI_53806"},{"id":"A105","pred":"chebi_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/CHEBI_61484"},{"id":"A106","pred":"chebi_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/CHEBI_74790"},{"id":"A107","pred":"chebi_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"},{"id":"A108","pred":"chebi_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A109","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_74327"}],"text":"The discontinuous epitopes in the spike protein of the Indian SARS-CoV-2 were further identified using multiple methods, Ellipro and DiscoTope. Conformational epitopes based on these methods were mapped on the pre-fusion structure of the modelled Indian SARS-CoV-2 spike protein. The newly released structure of the SARS-CoV-2 spike protein was used as the template for modelling the Indian spike protein. Ramachandran plot statistics revealed 83.7 per cent of the residues to be in the core region, 14.4 per cent in the additionally allowed region and 0.5 per cent in the disallowed region. Four epitopes were predicted by Ellipro based on the PI threshold of 0.8 (Supplementary Table II (available from http:/ /www. ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm7.pdf)). The result from the DiscoTope is presented in Supplementary Table III (available from http://www.ijmr.org.in/articles/ 2020/151/2/ images/ IndianJMedRes_2020_151_2_200_281471_sm8.pdf). The mapped conformational epitopes are depicted in Figure 2. For the purpose of comparison, the Indian S protein sequence was also modelled using the pre-fusion structure of SARS-CoV-1 (6ACC.PDB; 87.29% identity), and the results for the conformational epitopes predicted are in Supplementary Table IV (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_28147 1_sm9.pdf and Supplementary Figure 2 (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm10.pdf)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T153","span":{"begin":144,"end":279},"obj":"Sentence"},{"id":"T154","span":{"begin":280,"end":405},"obj":"Sentence"},{"id":"T155","span":{"begin":406,"end":591},"obj":"Sentence"},{"id":"T156","span":{"begin":592,"end":803},"obj":"Sentence"},{"id":"T157","span":{"begin":804,"end":988},"obj":"Sentence"},{"id":"T158","span":{"begin":989,"end":1049},"obj":"Sentence"},{"id":"T159","span":{"begin":1050,"end":1541},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The discontinuous epitopes in the spike protein of the Indian SARS-CoV-2 were further identified using multiple methods, Ellipro and DiscoTope. Conformational epitopes based on these methods were mapped on the pre-fusion structure of the modelled Indian SARS-CoV-2 spike protein. The newly released structure of the SARS-CoV-2 spike protein was used as the template for modelling the Indian spike protein. Ramachandran plot statistics revealed 83.7 per cent of the residues to be in the core region, 14.4 per cent in the additionally allowed region and 0.5 per cent in the disallowed region. Four epitopes were predicted by Ellipro based on the PI threshold of 0.8 (Supplementary Table II (available from http:/ /www. ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm7.pdf)). The result from the DiscoTope is presented in Supplementary Table III (available from http://www.ijmr.org.in/articles/ 2020/151/2/ images/ IndianJMedRes_2020_151_2_200_281471_sm8.pdf). The mapped conformational epitopes are depicted in Figure 2. For the purpose of comparison, the Indian S protein sequence was also modelled using the pre-fusion structure of SARS-CoV-1 (6ACC.PDB; 87.29% identity), and the results for the conformational epitopes predicted are in Supplementary Table IV (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_28147 1_sm9.pdf and Supplementary Figure 2 (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm10.pdf)."}