PMC:7784829 / 6368-7113 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7784829","sourcedb":"PMC","sourceid":"7784829","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7784829","text":"Preparation of coordinate file\nThe X-ray crystal structure of spike surface glycoprotein of SARS-CoV (PDB entry: 6CRV, resolution = 3.2 Å) and co-crystallized structure of SARS-CoV-2 RBD with human ACE2 Protein (PDB entry: 6M0J, resolution = 2.45 Å) was retrieved from Protein Data Bank (https:/www.rscb.org/pdb). The protein structure was prepared using the Discovery Studio Visualizer (version 3.1) and AutoDock Tools (ADT; version 1.5.4) through different steps viz. removal of water molecules and co-crystallized ligand, addition of missing hydrogen atoms, addition of Gasteiger-Marsili and Kollman charges, merging of non-polar hydrogens, and assignment of rotatable bonds. The file was then saved in pdbqt file format for further analysis.","divisions":[{"label":"title","span":{"begin":0,"end":30}}],"tracks":[{"project":"LitCovid-sentences","denotations":[{"id":"T50","span":{"begin":0,"end":30},"obj":"Sentence"},{"id":"T51","span":{"begin":31,"end":112},"obj":"Sentence"},{"id":"T52","span":{"begin":113,"end":222},"obj":"Sentence"},{"id":"T53","span":{"begin":223,"end":313},"obj":"Sentence"},{"id":"T54","span":{"begin":314,"end":678},"obj":"Sentence"},{"id":"T55","span":{"begin":679,"end":745},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T50","pred":"source","obj":"LitCovid-sentences"},{"subj":"T51","pred":"source","obj":"LitCovid-sentences"},{"subj":"T52","pred":"source","obj":"LitCovid-sentences"},{"subj":"T53","pred":"source","obj":"LitCovid-sentences"},{"subj":"T54","pred":"source","obj":"LitCovid-sentences"},{"subj":"T55","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"177","span":{"begin":198,"end":202},"obj":"Gene"},{"id":"178","span":{"begin":282,"end":286},"obj":"Gene"},{"id":"179","span":{"begin":92,"end":100},"obj":"Species"},{"id":"180","span":{"begin":172,"end":182},"obj":"Species"},{"id":"181","span":{"begin":192,"end":197},"obj":"Species"},{"id":"182","span":{"begin":481,"end":486},"obj":"Chemical"},{"id":"183","span":{"begin":545,"end":553},"obj":"Chemical"},{"id":"184","span":{"begin":633,"end":642},"obj":"Chemical"},{"id":"185","span":{"begin":573,"end":590},"obj":"Disease"}],"attributes":[{"id":"A177","pred":"tao:has_database_id","subj":"177","obj":"Gene:59272"},{"id":"A178","pred":"tao:has_database_id","subj":"178","obj":"Gene:55024"},{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Tax:694009"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Tax:2697049"},{"id":"A181","pred":"tao:has_database_id","subj":"181","obj":"Tax:9606"},{"id":"A182","pred":"tao:has_database_id","subj":"182","obj":"MESH:D014867"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"MESH:D006859"},{"id":"A184","pred":"tao:has_database_id","subj":"184","obj":"MESH:D006859"},{"subj":"177","pred":"source","obj":"LitCovid-PubTator"},{"subj":"178","pred":"source","obj":"LitCovid-PubTator"},{"subj":"179","pred":"source","obj":"LitCovid-PubTator"},{"subj":"180","pred":"source","obj":"LitCovid-PubTator"},{"subj":"181","pred":"source","obj":"LitCovid-PubTator"},{"subj":"182","pred":"source","obj":"LitCovid-PubTator"},{"subj":"183","pred":"source","obj":"LitCovid-PubTator"},{"subj":"184","pred":"source","obj":"LitCovid-PubTator"},{"subj":"185","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-sentences","color":"#e093ec","default":true},{"id":"LitCovid-PubTator","color":"#93ecc6"}]}]}}