PMC:7111504 / 20983-21502 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"312","span":{"begin":16,"end":25},"obj":"Species"},{"id":"313","span":{"begin":168,"end":177},"obj":"Chemical"},{"id":"314","span":{"begin":368,"end":377},"obj":"Chemical"},{"id":"315","span":{"begin":388,"end":389},"obj":"Chemical"}],"attributes":[{"id":"A312","pred":"tao:has_database_id","subj":"312","obj":"Tax:2697049"},{"id":"A315","pred":"tao:has_database_id","subj":"315","obj":"MESH:D007930"}],"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":"We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 4)."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T217","span":{"begin":16,"end":25},"obj":"SP_7"},{"id":"T218","span":{"begin":26,"end":31},"obj":"NCBITaxon:10239"},{"id":"T219","span":{"begin":108,"end":112},"obj":"SP_9"},{"id":"T80024","span":{"begin":16,"end":25},"obj":"SP_7"},{"id":"T4859","span":{"begin":26,"end":31},"obj":"NCBITaxon:10239"},{"id":"T7055","span":{"begin":108,"end":112},"obj":"SP_9"}],"text":"We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 4)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T105","span":{"begin":32,"end":39},"obj":"Body_part"},{"id":"T106","span":{"begin":399,"end":410},"obj":"Body_part"}],"attributes":[{"id":"A105","pred":"fma_id","subj":"T105","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A106","pred":"fma_id","subj":"T106","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 4)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T259","span":{"begin":26,"end":31},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T260","span":{"begin":62,"end":63},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T261","span":{"begin":65,"end":66},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T262","span":{"begin":118,"end":119},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T263","span":{"begin":276,"end":284},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T264","span":{"begin":301,"end":302},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 4)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T145","span":{"begin":32,"end":39},"obj":"Chemical"},{"id":"T146","span":{"begin":276,"end":284},"obj":"Chemical"},{"id":"T147","span":{"begin":399,"end":410},"obj":"Chemical"},{"id":"T148","span":{"begin":399,"end":404},"obj":"Chemical"},{"id":"T149","span":{"begin":405,"end":410},"obj":"Chemical"}],"attributes":[{"id":"A145","pred":"chebi_id","subj":"T145","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A146","pred":"chebi_id","subj":"T146","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A147","pred":"chebi_id","subj":"T147","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A148","pred":"chebi_id","subj":"T148","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A149","pred":"chebi_id","subj":"T149","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"}],"text":"We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 4)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T221","span":{"begin":0,"end":143},"obj":"Sentence"},{"id":"T222","span":{"begin":144,"end":232},"obj":"Sentence"},{"id":"T223","span":{"begin":233,"end":431},"obj":"Sentence"},{"id":"T224","span":{"begin":432,"end":519},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 4)."}