PMC:7441777 / 13257-13859 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"2.1.4. Protein-ligand interactions\nLigPlot+ was used to investigate protein-ligand interactions for a given .pdb file containing the docked conformation and also the final simulated conformation (Wallace et al., 1995). The LigPlot+ program self-generated schematic 2D representations of protein-ligand interaction. The output file represents the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic contacts, and atom accessibilities. H-bonds are shown in green dotted lines, whereas residues involved in hydrophobic interaction are represented in the red semicircle.","divisions":[{"label":"label","span":{"begin":0,"end":6}},{"label":"title","span":{"begin":8,"end":35}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T28","span":{"begin":8,"end":15},"obj":"Body_part"},{"id":"T29","span":{"begin":69,"end":76},"obj":"Body_part"},{"id":"T30","span":{"begin":288,"end":295},"obj":"Body_part"}],"attributes":[{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma67257"},{"subj":"T28","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T29","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T30","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T91","span":{"begin":101,"end":102},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T91","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T218","span":{"begin":8,"end":15},"obj":"Chemical"},{"id":"T219","span":{"begin":16,"end":22},"obj":"Chemical"},{"id":"T220","span":{"begin":69,"end":76},"obj":"Chemical"},{"id":"T221","span":{"begin":77,"end":83},"obj":"Chemical"},{"id":"T222","span":{"begin":288,"end":295},"obj":"Chemical"},{"id":"T223","span":{"begin":296,"end":302},"obj":"Chemical"},{"id":"T224","span":{"begin":406,"end":414},"obj":"Chemical"},{"id":"T225","span":{"begin":448,"end":452},"obj":"Chemical"}],"attributes":[{"id":"A218","pred":"chebi_id","subj":"T218","obj":"http://purl.obolibrary.org/obo/CHEBI_16541"},{"id":"A219","pred":"chebi_id","subj":"T219","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A220","pred":"chebi_id","subj":"T220","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A221","pred":"chebi_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A222","pred":"chebi_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A223","pred":"chebi_id","subj":"T223","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A224","pred":"chebi_id","subj":"T224","obj":"http://purl.obolibrary.org/obo/CHEBI_49637"},{"id":"A225","pred":"chebi_id","subj":"T225","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"subj":"T218","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T219","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T220","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T221","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T222","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T223","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T224","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T225","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"351","span":{"begin":406,"end":414},"obj":"Chemical"}],"attributes":[{"id":"A351","pred":"tao:has_database_id","subj":"351","obj":"MESH:D006859"},{"subj":"351","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_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T143","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T144","span":{"begin":8,"end":35},"obj":"Sentence"},{"id":"T145","span":{"begin":36,"end":219},"obj":"Sentence"},{"id":"T146","span":{"begin":220,"end":315},"obj":"Sentence"},{"id":"T147","span":{"begin":316,"end":469},"obj":"Sentence"},{"id":"T148","span":{"begin":470,"end":602},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T143","pred":"source","obj":"LitCovid-sentences"},{"subj":"T144","pred":"source","obj":"LitCovid-sentences"},{"subj":"T145","pred":"source","obj":"LitCovid-sentences"},{"subj":"T146","pred":"source","obj":"LitCovid-sentences"},{"subj":"T147","pred":"source","obj":"LitCovid-sentences"},{"subj":"T148","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32720577-7630882-56195104","span":{"begin":213,"end":217},"obj":"7630882"}],"attributes":[{"subj":"32720577-7630882-56195104","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#d293ec","default":true},{"id":"LitCovid-PD-CLO","color":"#93ecb8"},{"id":"LitCovid-PD-CHEBI","color":"#ec9e93"},{"id":"LitCovid-PubTator","color":"#93a1ec"},{"id":"LitCovid-sentences","color":"#bbec93"},{"id":"2_test","color":"#ec93d5"}]}]}}