PMC:7553147 / 4318-5470 JSONTXT

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T6","span":{"begin":492,"end":500},"obj":"Disease"},{"id":"T7","span":{"begin":576,"end":584},"obj":"Disease"},{"id":"T8","span":{"begin":672,"end":680},"obj":"Disease"},{"id":"T9","span":{"begin":809,"end":817},"obj":"Disease"}],"attributes":[{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"In this work, we describe the new structural information that has been obtained and how it impacts our biological understanding of the system, together with the new workflows and algorithms that have made this accomplishment possible. We used Scipion 2.0 (de la Rosa-Trevín et al., 2016 ▸) in order to easily combine different software suites in the analysis workflows. Maps and models have been deposited in public databases [EMPIAR (Iudin et al., 2016 ▸) and EMDB (Lawson et al., 2011 ▸)]: SARS-CoV-2 spike in the prefusion state as EMDB entry EMD-11328 and PDB entry 6zow, SARS-CoV-2 stabilized spike in the prefusion state (1-up conformation) as EMDB entry EMD-11341, SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up closed conformation) as EMDB entry EMD-11336 and PDB entry 6zp5, and SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up open conformation) as EMDB entry EMD-11337 and PDB entry 6zp7. All of the used data, the image-processing workflow and the intermediate results were also uploaded to EMPIAR (entries EMPIAR-10514 and EMPIAR-10516) by running the EMPIAR automatic deposition feature in Scipion."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T31","span":{"begin":62,"end":65},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"}],"text":"In this work, we describe the new structural information that has been obtained and how it impacts our biological understanding of the system, together with the new workflows and algorithms that have made this accomplishment possible. We used Scipion 2.0 (de la Rosa-Trevín et al., 2016 ▸) in order to easily combine different software suites in the analysis workflows. Maps and models have been deposited in public databases [EMPIAR (Iudin et al., 2016 ▸) and EMDB (Lawson et al., 2011 ▸)]: SARS-CoV-2 spike in the prefusion state as EMDB entry EMD-11328 and PDB entry 6zow, SARS-CoV-2 stabilized spike in the prefusion state (1-up conformation) as EMDB entry EMD-11341, SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up closed conformation) as EMDB entry EMD-11336 and PDB entry 6zp5, and SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up open conformation) as EMDB entry EMD-11337 and PDB entry 6zp7. All of the used data, the image-processing workflow and the intermediate results were also uploaded to EMPIAR (entries EMPIAR-10514 and EMPIAR-10516) by running the EMPIAR automatic deposition feature in Scipion."}

{"project":"LitCovid-sentences","denotations":[{"id":"T27","span":{"begin":0,"end":234},"obj":"Sentence"},{"id":"T28","span":{"begin":235,"end":369},"obj":"Sentence"},{"id":"T29","span":{"begin":370,"end":939},"obj":"Sentence"},{"id":"T30","span":{"begin":940,"end":1152},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In this work, we describe the new structural information that has been obtained and how it impacts our biological understanding of the system, together with the new workflows and algorithms that have made this accomplishment possible. We used Scipion 2.0 (de la Rosa-Trevín et al., 2016 ▸) in order to easily combine different software suites in the analysis workflows. Maps and models have been deposited in public databases [EMPIAR (Iudin et al., 2016 ▸) and EMDB (Lawson et al., 2011 ▸)]: SARS-CoV-2 spike in the prefusion state as EMDB entry EMD-11328 and PDB entry 6zow, SARS-CoV-2 stabilized spike in the prefusion state (1-up conformation) as EMDB entry EMD-11341, SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up closed conformation) as EMDB entry EMD-11336 and PDB entry 6zp5, and SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up open conformation) as EMDB entry EMD-11337 and PDB entry 6zp7. All of the used data, the image-processing workflow and the intermediate results were also uploaded to EMPIAR (entries EMPIAR-10514 and EMPIAR-10516) by running the EMPIAR automatic deposition feature in Scipion."}

{"project":"LitCovid-PubTator","denotations":[{"id":"39","span":{"begin":820,"end":825},"obj":"Gene"},{"id":"40","span":{"begin":683,"end":688},"obj":"Gene"},{"id":"41","span":{"begin":598,"end":603},"obj":"Gene"},{"id":"42","span":{"begin":503,"end":508},"obj":"Gene"},{"id":"43","span":{"begin":492,"end":502},"obj":"Species"},{"id":"44","span":{"begin":576,"end":586},"obj":"Species"},{"id":"45","span":{"begin":672,"end":682},"obj":"Species"},{"id":"46","span":{"begin":809,"end":819},"obj":"Species"},{"id":"47","span":{"begin":764,"end":784},"obj":"Disease"}],"attributes":[{"id":"A39","pred":"tao:has_database_id","subj":"39","obj":"Gene:43740568"},{"id":"A40","pred":"tao:has_database_id","subj":"40","obj":"Gene:43740568"},{"id":"A41","pred":"tao:has_database_id","subj":"41","obj":"Gene:43740568"},{"id":"A42","pred":"tao:has_database_id","subj":"42","obj":"Gene:43740568"},{"id":"A43","pred":"tao:has_database_id","subj":"43","obj":"Tax:2697049"},{"id":"A44","pred":"tao:has_database_id","subj":"44","obj":"Tax:2697049"},{"id":"A45","pred":"tao:has_database_id","subj":"45","obj":"Tax:2697049"},{"id":"A46","pred":"tao:has_database_id","subj":"46","obj":"Tax:2697049"},{"id":"A47","pred":"tao:has_database_id","subj":"47","obj":"MESH:C557826"}],"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":"In this work, we describe the new structural information that has been obtained and how it impacts our biological understanding of the system, together with the new workflows and algorithms that have made this accomplishment possible. We used Scipion 2.0 (de la Rosa-Trevín et al., 2016 ▸) in order to easily combine different software suites in the analysis workflows. Maps and models have been deposited in public databases [EMPIAR (Iudin et al., 2016 ▸) and EMDB (Lawson et al., 2011 ▸)]: SARS-CoV-2 spike in the prefusion state as EMDB entry EMD-11328 and PDB entry 6zow, SARS-CoV-2 stabilized spike in the prefusion state (1-up conformation) as EMDB entry EMD-11341, SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up closed conformation) as EMDB entry EMD-11336 and PDB entry 6zp5, and SARS-CoV-2 spike in the prefusion state (flexibility analysis, 1-up open conformation) as EMDB entry EMD-11337 and PDB entry 6zp7. All of the used data, the image-processing workflow and the intermediate results were also uploaded to EMPIAR (entries EMPIAR-10514 and EMPIAR-10516) by running the EMPIAR automatic deposition feature in Scipion."}