PMC:7111504 / 10164-12359 JSONTXT

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    LitCovid-PubTator

    {"project":"LitCovid-PubTator","denotations":[{"id":"135","span":{"begin":42,"end":51},"obj":"Species"},{"id":"145","span":{"begin":564,"end":569},"obj":"Gene"},{"id":"146","span":{"begin":577,"end":582},"obj":"Gene"},{"id":"147","span":{"begin":590,"end":595},"obj":"Gene"},{"id":"148","span":{"begin":603,"end":608},"obj":"Gene"},{"id":"149","span":{"begin":619,"end":624},"obj":"Gene"},{"id":"150","span":{"begin":386,"end":389},"obj":"Gene"},{"id":"151","span":{"begin":167,"end":176},"obj":"Species"},{"id":"152","span":{"begin":219,"end":228},"obj":"Species"},{"id":"153","span":{"begin":428,"end":437},"obj":"Chemical"},{"id":"155","span":{"begin":666,"end":669},"obj":"Gene"},{"id":"158","span":{"begin":1061,"end":1070},"obj":"Species"},{"id":"159","span":{"begin":1131,"end":1140},"obj":"Chemical"},{"id":"162","span":{"begin":1980,"end":1983},"obj":"Gene"},{"id":"163","span":{"begin":1956,"end":1965},"obj":"Species"},{"id":"171","span":{"begin":2031,"end":2034},"obj":"Gene"},{"id":"172","span":{"begin":2061,"end":2066},"obj":"Gene"},{"id":"173","span":{"begin":2074,"end":2079},"obj":"Gene"},{"id":"174","span":{"begin":2087,"end":2092},"obj":"Gene"},{"id":"175","span":{"begin":2100,"end":2105},"obj":"Gene"},{"id":"176","span":{"begin":2116,"end":2121},"obj":"Gene"},{"id":"177","span":{"begin":2139,"end":2148},"obj":"Chemical"}],"attributes":[{"id":"A135","pred":"tao:has_database_id","subj":"135","obj":"Tax:2697049"},{"id":"A145","pred":"tao:has_database_id","subj":"145","obj":"Gene:3105"},{"id":"A146","pred":"tao:has_database_id","subj":"146","obj":"Gene:3105"},{"id":"A147","pred":"tao:has_database_id","subj":"147","obj":"Gene:3106"},{"id":"A148","pred":"tao:has_database_id","subj":"148","obj":"Gene:3106"},{"id":"A149","pred":"tao:has_database_id","subj":"149","obj":"Gene:3107"},{"id":"A150","pred":"tao:has_database_id","subj":"150","obj":"Gene:3107"},{"id":"A151","pred":"tao:has_database_id","subj":"151","obj":"Tax:2697049"},{"id":"A152","pred":"tao:has_database_id","subj":"152","obj":"Tax:2697049"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Gene:3107"},{"id":"A158","pred":"tao:has_database_id","subj":"158","obj":"Tax:2697049"},{"id":"A162","pred":"tao:has_database_id","subj":"162","obj":"Gene:3107"},{"id":"A163","pred":"tao:has_database_id","subj":"163","obj":"Tax:2697049"},{"id":"A171","pred":"tao:has_database_id","subj":"171","obj":"Gene:3107"},{"id":"A172","pred":"tao:has_database_id","subj":"172","obj":"Gene:3105"},{"id":"A173","pred":"tao:has_database_id","subj":"173","obj":"Gene:3105"},{"id":"A174","pred":"tao:has_database_id","subj":"174","obj":"Gene:3106"},{"id":"A175","pred":"tao:has_database_id","subj":"175","obj":"Gene:3106"},{"id":"A176","pred":"tao:has_database_id","subj":"176","obj":"Gene:3107"}],"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":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    LitCovid-PMC-OGER-BB

    {"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T111","span":{"begin":18,"end":29},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T112","span":{"begin":42,"end":51},"obj":"SP_7"},{"id":"T113","span":{"begin":134,"end":145},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T114","span":{"begin":167,"end":176},"obj":"SP_7"},{"id":"T115","span":{"begin":209,"end":213},"obj":"SP_9"},{"id":"T116","span":{"begin":219,"end":228},"obj":"SP_7"},{"id":"T117","span":{"begin":322,"end":336},"obj":"BV_15"},{"id":"T118","span":{"begin":386,"end":389},"obj":"GO:0042611"},{"id":"T119","span":{"begin":495,"end":505},"obj":"SO:0001024"},{"id":"T120","span":{"begin":564,"end":569},"obj":"PR:000002009"},{"id":"T121","span":{"begin":577,"end":582},"obj":"PR:000002009"},{"id":"T122","span":{"begin":590,"end":595},"obj":"PR:000002010"},{"id":"T123","span":{"begin":603,"end":608},"obj":"PR:000002010"},{"id":"T124","span":{"begin":619,"end":624},"obj":"PR:000002011"},{"id":"T125","span":{"begin":631,"end":638},"obj":"SO:0001023"},{"id":"T126","span":{"begin":666,"end":669},"obj":"GO:0042611"},{"id":"T127","span":{"begin":687,"end":701},"obj":"BV_15"},{"id":"T128","span":{"begin":771,"end":778},"obj":"SO:0001023"},{"id":"T129","span":{"begin":801,"end":815},"obj":"BV_15"},{"id":"T130","span":{"begin":897,"end":911},"obj":"BV_15"},{"id":"T131","span":{"begin":991,"end":1002},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T132","span":{"begin":1061,"end":1070},"obj":"SP_7"},{"id":"T133","span":{"begin":1120,"end":1127},"obj":"SO:0001023"},{"id":"T134","span":{"begin":1182,"end":1189},"obj":"SO:0001023"},{"id":"T135","span":{"begin":1194,"end":1208},"obj":"BV_15"},{"id":"T136","span":{"begin":1245,"end":1252},"obj":"SO:0001023"},{"id":"T137","span":{"begin":1325,"end":1331},"obj":"SO:0001023"},{"id":"T138","span":{"begin":1956,"end":1965},"obj":"SP_7"},{"id":"T139","span":{"begin":1980,"end":1983},"obj":"GO:0042611"},{"id":"T140","span":{"begin":2001,"end":2015},"obj":"BV_15"},{"id":"T141","span":{"begin":2031,"end":2034},"obj":"GO:0042611"},{"id":"T142","span":{"begin":2061,"end":2066},"obj":"PR:000002009"},{"id":"T143","span":{"begin":2074,"end":2079},"obj":"PR:000002009"},{"id":"T144","span":{"begin":2087,"end":2092},"obj":"PR:000002010"},{"id":"T145","span":{"begin":2100,"end":2105},"obj":"PR:000002010"},{"id":"T146","span":{"begin":2116,"end":2121},"obj":"PR:000002011"},{"id":"T147","span":{"begin":2128,"end":2135},"obj":"SO:0001023"},{"id":"T148","span":{"begin":2157,"end":2171},"obj":"BV_15"},{"id":"T62473","span":{"begin":18,"end":29},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T49303","span":{"begin":42,"end":51},"obj":"SP_7"},{"id":"T4279","span":{"begin":134,"end":145},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T6626","span":{"begin":167,"end":176},"obj":"SP_7"},{"id":"T90148","span":{"begin":209,"end":213},"obj":"SP_9"},{"id":"T85766","span":{"begin":219,"end":228},"obj":"SP_7"},{"id":"T90107","span":{"begin":322,"end":336},"obj":"BV_15"},{"id":"T45797","span":{"begin":386,"end":389},"obj":"GO:0042611"},{"id":"T63293","span":{"begin":495,"end":505},"obj":"SO:0001024"},{"id":"T59388","span":{"begin":564,"end":569},"obj":"PR:000002009"},{"id":"T64753","span":{"begin":577,"end":582},"obj":"PR:000002009"},{"id":"T67356","span":{"begin":590,"end":595},"obj":"PR:000002010"},{"id":"T99742","span":{"begin":603,"end":608},"obj":"PR:000002010"},{"id":"T8696","span":{"begin":619,"end":624},"obj":"PR:000002011"},{"id":"T3771","span":{"begin":631,"end":638},"obj":"SO:0001023"},{"id":"T81007","span":{"begin":666,"end":669},"obj":"GO:0042611"},{"id":"T71652","span":{"begin":687,"end":701},"obj":"BV_15"},{"id":"T43291","span":{"begin":771,"end":778},"obj":"SO:0001023"},{"id":"T65127","span":{"begin":801,"end":815},"obj":"BV_15"},{"id":"T76335","span":{"begin":897,"end":911},"obj":"BV_15"},{"id":"T29057","span":{"begin":991,"end":1002},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T69709","span":{"begin":1061,"end":1070},"obj":"SP_7"},{"id":"T97652","span":{"begin":1120,"end":1127},"obj":"SO:0001023"},{"id":"T30189","span":{"begin":1182,"end":1189},"obj":"SO:0001023"},{"id":"T17570","span":{"begin":1194,"end":1208},"obj":"BV_15"},{"id":"T56623","span":{"begin":1245,"end":1252},"obj":"SO:0001023"},{"id":"T32084","span":{"begin":1325,"end":1331},"obj":"SO:0001023"},{"id":"T12377","span":{"begin":1956,"end":1965},"obj":"SP_7"},{"id":"T98397","span":{"begin":1980,"end":1983},"obj":"GO:0042611"},{"id":"T94145","span":{"begin":2001,"end":2015},"obj":"BV_15"},{"id":"T75496","span":{"begin":2031,"end":2034},"obj":"GO:0042611"},{"id":"T7224","span":{"begin":2061,"end":2066},"obj":"PR:000002009"},{"id":"T38753","span":{"begin":2074,"end":2079},"obj":"PR:000002009"},{"id":"T92877","span":{"begin":2087,"end":2092},"obj":"PR:000002010"},{"id":"T36156","span":{"begin":2100,"end":2105},"obj":"PR:000002010"},{"id":"T68789","span":{"begin":2116,"end":2121},"obj":"PR:000002011"},{"id":"T46318","span":{"begin":2128,"end":2135},"obj":"SO:0001023"},{"id":"T4457","span":{"begin":2157,"end":2171},"obj":"BV_15"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    LitCovid-PD-FMA-UBERON

    {"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T55","span":{"begin":257,"end":268},"obj":"Body_part"},{"id":"T56","span":{"begin":290,"end":300},"obj":"Body_part"},{"id":"T57","span":{"begin":386,"end":389},"obj":"Body_part"},{"id":"T58","span":{"begin":456,"end":459},"obj":"Body_part"},{"id":"T59","span":{"begin":564,"end":567},"obj":"Body_part"},{"id":"T60","span":{"begin":577,"end":580},"obj":"Body_part"},{"id":"T61","span":{"begin":590,"end":593},"obj":"Body_part"},{"id":"T62","span":{"begin":603,"end":606},"obj":"Body_part"},{"id":"T63","span":{"begin":619,"end":622},"obj":"Body_part"},{"id":"T64","span":{"begin":666,"end":669},"obj":"Body_part"},{"id":"T65","span":{"begin":767,"end":770},"obj":"Body_part"},{"id":"T66","span":{"begin":879,"end":882},"obj":"Body_part"},{"id":"T67","span":{"begin":1116,"end":1119},"obj":"Body_part"},{"id":"T68","span":{"begin":1178,"end":1181},"obj":"Body_part"},{"id":"T69","span":{"begin":1321,"end":1324},"obj":"Body_part"},{"id":"T70","span":{"begin":1424,"end":1427},"obj":"Body_part"},{"id":"T71","span":{"begin":1980,"end":1983},"obj":"Body_part"},{"id":"T72","span":{"begin":2031,"end":2034},"obj":"Body_part"},{"id":"T73","span":{"begin":2061,"end":2064},"obj":"Body_part"},{"id":"T74","span":{"begin":2074,"end":2077},"obj":"Body_part"},{"id":"T75","span":{"begin":2087,"end":2090},"obj":"Body_part"},{"id":"T76","span":{"begin":2100,"end":2103},"obj":"Body_part"},{"id":"T77","span":{"begin":2116,"end":2119},"obj":"Body_part"}],"attributes":[{"id":"A55","pred":"fma_id","subj":"T55","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A69","pred":"fma_id","subj":"T69","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A75","pred":"fma_id","subj":"T75","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A76","pred":"fma_id","subj":"T76","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A77","pred":"fma_id","subj":"T77","obj":"http://purl.org/sig/ont/fma/fma84795"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    LitCovid-PD-MONDO

    {"project":"LitCovid-PD-MONDO","denotations":[{"id":"T14","span":{"begin":1366,"end":1368},"obj":"Disease"},{"id":"T15","span":{"begin":1376,"end":1378},"obj":"Disease"},{"id":"T16","span":{"begin":1386,"end":1388},"obj":"Disease"},{"id":"T17","span":{"begin":1396,"end":1398},"obj":"Disease"},{"id":"T18","span":{"begin":1406,"end":1408},"obj":"Disease"}],"attributes":[{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005072"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005072"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0005072"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005072"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005072"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    LitCovid-PD-CLO

    {"project":"LitCovid-PD-CLO","denotations":[{"id":"T137","span":{"begin":30,"end":38},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T138","span":{"begin":64,"end":65},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T139","span":{"begin":114,"end":115},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T140","span":{"begin":146,"end":154},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T141","span":{"begin":243,"end":244},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T142","span":{"begin":346,"end":354},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T143","span":{"begin":484,"end":491},"obj":"http://purl.obolibrary.org/obo/CLO_0009985"},{"id":"T144","span":{"begin":568,"end":569},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T145","span":{"begin":581,"end":582},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T146","span":{"begin":594,"end":595},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T147","span":{"begin":607,"end":608},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T148","span":{"begin":651,"end":654},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"},{"id":"T149","span":{"begin":728,"end":736},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T150","span":{"begin":973,"end":974},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T151","span":{"begin":1077,"end":1085},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T152","span":{"begin":1452,"end":1456},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T153","span":{"begin":1458,"end":1465},"obj":"http://purl.obolibrary.org/obo/CLO_0053001"},{"id":"T154","span":{"begin":1490,"end":1494},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T155","span":{"begin":1496,"end":1503},"obj":"http://purl.obolibrary.org/obo/CLO_0053001"},{"id":"T156","span":{"begin":1525,"end":1529},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T157","span":{"begin":1563,"end":1567},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T158","span":{"begin":1600,"end":1604},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T159","span":{"begin":1685,"end":1689},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T160","span":{"begin":1790,"end":1794},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T161","span":{"begin":1828,"end":1832},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T162","span":{"begin":1869,"end":1873},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T163","span":{"begin":1966,"end":1974},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T164","span":{"begin":2065,"end":2066},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T165","span":{"begin":2078,"end":2079},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T166","span":{"begin":2091,"end":2092},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T167","span":{"begin":2104,"end":2105},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    LitCovid-PD-CHEBI

    {"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T74","span":{"begin":30,"end":38},"obj":"Chemical"},{"id":"T75","span":{"begin":146,"end":154},"obj":"Chemical"},{"id":"T76","span":{"begin":257,"end":268},"obj":"Chemical"},{"id":"T77","span":{"begin":257,"end":262},"obj":"Chemical"},{"id":"T78","span":{"begin":263,"end":268},"obj":"Chemical"},{"id":"T79","span":{"begin":290,"end":300},"obj":"Chemical"},{"id":"T80","span":{"begin":290,"end":295},"obj":"Chemical"},{"id":"T81","span":{"begin":296,"end":300},"obj":"Chemical"},{"id":"T82","span":{"begin":346,"end":354},"obj":"Chemical"},{"id":"T83","span":{"begin":728,"end":736},"obj":"Chemical"},{"id":"T84","span":{"begin":1077,"end":1085},"obj":"Chemical"},{"id":"T85","span":{"begin":1966,"end":1974},"obj":"Chemical"}],"attributes":[{"id":"A74","pred":"chebi_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A75","pred":"chebi_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A76","pred":"chebi_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A77","pred":"chebi_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A78","pred":"chebi_id","subj":"T78","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A79","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A81","pred":"chebi_id","subj":"T81","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    LitCovid-sentences

    {"project":"LitCovid-sentences","denotations":[{"id":"T115","span":{"begin":0,"end":60},"obj":"Sentence"},{"id":"T116","span":{"begin":61,"end":195},"obj":"Sentence"},{"id":"T117","span":{"begin":196,"end":317},"obj":"Sentence"},{"id":"T118","span":{"begin":318,"end":466},"obj":"Sentence"},{"id":"T119","span":{"begin":467,"end":656},"obj":"Sentence"},{"id":"T120","span":{"begin":657,"end":835},"obj":"Sentence"},{"id":"T121","span":{"begin":836,"end":936},"obj":"Sentence"},{"id":"T122","span":{"begin":937,"end":1050},"obj":"Sentence"},{"id":"T123","span":{"begin":1051,"end":1059},"obj":"Sentence"},{"id":"T124","span":{"begin":1061,"end":1230},"obj":"Sentence"},{"id":"T125","span":{"begin":1231,"end":1332},"obj":"Sentence"},{"id":"T126","span":{"begin":1333,"end":1427},"obj":"Sentence"},{"id":"T127","span":{"begin":1428,"end":1465},"obj":"Sentence"},{"id":"T128","span":{"begin":1466,"end":1503},"obj":"Sentence"},{"id":"T129","span":{"begin":1504,"end":1541},"obj":"Sentence"},{"id":"T130","span":{"begin":1542,"end":1579},"obj":"Sentence"},{"id":"T131","span":{"begin":1580,"end":1616},"obj":"Sentence"},{"id":"T132","span":{"begin":1617,"end":1654},"obj":"Sentence"},{"id":"T133","span":{"begin":1655,"end":1692},"obj":"Sentence"},{"id":"T134","span":{"begin":1693,"end":1730},"obj":"Sentence"},{"id":"T135","span":{"begin":1731,"end":1768},"obj":"Sentence"},{"id":"T136","span":{"begin":1769,"end":1806},"obj":"Sentence"},{"id":"T137","span":{"begin":1807,"end":1844},"obj":"Sentence"},{"id":"T138","span":{"begin":1845,"end":1882},"obj":"Sentence"},{"id":"T139","span":{"begin":1883,"end":1920},"obj":"Sentence"},{"id":"T140","span":{"begin":1921,"end":1930},"obj":"Sentence"},{"id":"T141","span":{"begin":1932,"end":2026},"obj":"Sentence"},{"id":"T142","span":{"begin":2027,"end":2195},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    MyTest

    {"project":"MyTest","denotations":[{"id":"32269766-28978689-30420972","span":{"begin":442,"end":444},"obj":"28978689"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}

    2_test

    {"project":"2_test","denotations":[{"id":"32269766-28978689-30420972","span":{"begin":442,"end":443},"obj":"28978689"}],"text":"De novo search of immunogenic peptides in 2019-nCoV proteome\nAs a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence. We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total). The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types. In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).\nBased on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3). For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3). Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.\nTable 3. 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.\nFor different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.\nAntigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA\nVQMAPISAM 0.893938 0 1 1 1 1 4\nAMYTPHTVL 0.862427 0 1 1 1 1 4\nTLDSKTQSL 0.254998 1 1 1 0 1 4\nKVDGVVQQL 0.191786 1 1 1 0 1 4\nKVDGVDVEL 0.18632 1 1 1 0 1 4\nMADQAMTQM 0.991227 1 0 1 0 1 3\nLEAPFLYLY 0.983072 1 0 0 1 1 3\nRTAPHGHVM 0.972153 1 0 1 0 1 3\nIPFAMQMAY 0.961569 1 0 1 0 1 3\nFLTENLLLY 0.951715 1 1 0 0 1 3\nYLQPRTFLL 0.947743 1 1 0 0 1 3\nMMISAGFSL 0.941318 0 1 1 0 1 3\nATLPKGIMM 0.926603 1 0 1 0 1 3\nFigure 3. De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.\nThe MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred."}