PMC:7544943 / 32521-33299 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7544943","sourcedb":"PMC","sourceid":"7544943","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7544943","text":"3.6.4. Number of hydrogen bonds\nThe number of hydrogen bonds formed between the protein–ligand complex is the measure of the binding strength of the ligand to the protein. The RBD Spro (red) and Mpro (blue) bound to Piperine have a constant number of 1–2 hydrogen bonds throughout the simulation time (Figure 7(c)). There is a maximum number of 3 and 4 hydrogen bonds observed in the case of RBD Spro-Piperine and Mpro-Piperine, respectively. The number of hydrogen bonds fluctuates throughout the simulation time for both RBD Spro-Piperine and Mpro-Piperine, which suggests for conformational changes in the binding site of the ligand during the simulation. The observation from hydrogen bond analysis indicates that the complexes are stable for the performed simulation time.","divisions":[{"label":"label","span":{"begin":0,"end":6}},{"label":"title","span":{"begin":8,"end":32}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T44","span":{"begin":81,"end":88},"obj":"Body_part"},{"id":"T45","span":{"begin":164,"end":171},"obj":"Body_part"}],"attributes":[{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma67257"},{"subj":"T44","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T45","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T157","span":{"begin":231,"end":232},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T158","span":{"begin":326,"end":327},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T157","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T158","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"763","span":{"begin":18,"end":26},"obj":"Chemical"},{"id":"776","span":{"begin":196,"end":200},"obj":"Gene"},{"id":"777","span":{"begin":546,"end":550},"obj":"Gene"},{"id":"778","span":{"begin":415,"end":419},"obj":"Gene"},{"id":"779","span":{"begin":47,"end":55},"obj":"Chemical"},{"id":"780","span":{"begin":217,"end":225},"obj":"Chemical"},{"id":"781","span":{"begin":256,"end":264},"obj":"Chemical"},{"id":"782","span":{"begin":354,"end":362},"obj":"Chemical"},{"id":"783","span":{"begin":397,"end":410},"obj":"Chemical"},{"id":"784","span":{"begin":458,"end":466},"obj":"Chemical"},{"id":"785","span":{"begin":524,"end":527},"obj":"Chemical"},{"id":"786","span":{"begin":528,"end":541},"obj":"Chemical"},{"id":"787","span":{"begin":681,"end":689},"obj":"Chemical"}],"attributes":[{"id":"A763","pred":"tao:has_database_id","subj":"763","obj":"MESH:D006859"},{"id":"A776","pred":"tao:has_database_id","subj":"776","obj":"Gene:8673700"},{"id":"A777","pred":"tao:has_database_id","subj":"777","obj":"Gene:8673700"},{"id":"A778","pred":"tao:has_database_id","subj":"778","obj":"Gene:8673700"},{"id":"A779","pred":"tao:has_database_id","subj":"779","obj":"MESH:D006859"},{"id":"A780","pred":"tao:has_database_id","subj":"780","obj":"MESH:C008922"},{"id":"A781","pred":"tao:has_database_id","subj":"781","obj":"MESH:D006859"},{"id":"A782","pred":"tao:has_database_id","subj":"782","obj":"MESH:D006859"},{"id":"A784","pred":"tao:has_database_id","subj":"784","obj":"MESH:D006859"},{"id":"A787","pred":"tao:has_database_id","subj":"787","obj":"MESH:D006859"},{"subj":"763","pred":"source","obj":"LitCovid-PubTator"},{"subj":"776","pred":"source","obj":"LitCovid-PubTator"},{"subj":"777","pred":"source","obj":"LitCovid-PubTator"},{"subj":"778","pred":"source","obj":"LitCovid-PubTator"},{"subj":"779","pred":"source","obj":"LitCovid-PubTator"},{"subj":"780","pred":"source","obj":"LitCovid-PubTator"},{"subj":"781","pred":"source","obj":"LitCovid-PubTator"},{"subj":"782","pred":"source","obj":"LitCovid-PubTator"},{"subj":"783","pred":"source","obj":"LitCovid-PubTator"},{"subj":"784","pred":"source","obj":"LitCovid-PubTator"},{"subj":"785","pred":"source","obj":"LitCovid-PubTator"},{"subj":"786","pred":"source","obj":"LitCovid-PubTator"},{"subj":"787","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":"T282","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T283","span":{"begin":8,"end":32},"obj":"Sentence"},{"id":"T284","span":{"begin":33,"end":172},"obj":"Sentence"},{"id":"T285","span":{"begin":173,"end":316},"obj":"Sentence"},{"id":"T286","span":{"begin":317,"end":443},"obj":"Sentence"},{"id":"T287","span":{"begin":444,"end":659},"obj":"Sentence"},{"id":"T288","span":{"begin":660,"end":778},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T282","pred":"source","obj":"LitCovid-sentences"},{"subj":"T283","pred":"source","obj":"LitCovid-sentences"},{"subj":"T284","pred":"source","obj":"LitCovid-sentences"},{"subj":"T285","pred":"source","obj":"LitCovid-sentences"},{"subj":"T286","pred":"source","obj":"LitCovid-sentences"},{"subj":"T287","pred":"source","obj":"LitCovid-sentences"},{"subj":"T288","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#e693ec","default":true},{"id":"LitCovid-PD-CLO","color":"#93eccc"},{"id":"LitCovid-PubTator","color":"#ecb193"},{"id":"LitCovid-sentences","color":"#9793ec"}]}]}}