PMC:7755033 / 22622-23717 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7755033","sourcedb":"PMC","sourceid":"7755033","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7755033","text":"2.5.1. AutoDock\nMolecular docking of selected phytoconstituents of WS against human ACE2 receptor, SARS-CoV and SARS-CoV-2 target proteins was performed using AutoDock 4.0/ADT version 4.2.6 program (Morris et al., 1998) and further validated using two additional softwares viz. AutoDock vina and iGEMDOCK version 2.1 in order to investigate binding kinetics and binding modes to the refined proteins. Grid spacing was set at 0.375 Å and the grid points in the X, Y and Z axes were set to 60 × 60 × 60. The quest was based on the Lamarckian genetic algorithm (Miyamoto \u0026 Kollman, 1992; Oprea et al., 2001) and the binding energies of the results were subjected to further analysis.\nMolecular docking computation and visualization of binding interactions of withanolide analogs to human ACE2 receptor and selected SARS-CoV and SARS-CoV-2 protein targets was done using Accelrys Biovia Discovery Studio version 2017 R2. The best possible orientation of the ligand(s) in the protein binding pocket was selected for analysis on the basis of lowest binding energy (BE) and dissociation constant (Kd).","divisions":[{"label":"label","span":{"begin":0,"end":6}},{"label":"title","span":{"begin":8,"end":16}},{"label":"p","span":{"begin":17,"end":681}}],"tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"439","span":{"begin":85,"end":89},"obj":"Gene"},{"id":"440","span":{"begin":79,"end":84},"obj":"Species"},{"id":"441","span":{"begin":100,"end":108},"obj":"Species"},{"id":"442","span":{"begin":113,"end":123},"obj":"Species"},{"id":"443","span":{"begin":68,"end":70},"obj":"Species"},{"id":"450","span":{"begin":786,"end":790},"obj":"Gene"},{"id":"451","span":{"begin":780,"end":785},"obj":"Species"},{"id":"452","span":{"begin":813,"end":821},"obj":"Species"},{"id":"453","span":{"begin":826,"end":836},"obj":"Species"},{"id":"454","span":{"begin":757,"end":768},"obj":"Chemical"},{"id":"455","span":{"begin":1060,"end":1062},"obj":"Chemical"}],"attributes":[{"id":"A439","pred":"tao:has_database_id","subj":"439","obj":"Gene:59272"},{"id":"A440","pred":"tao:has_database_id","subj":"440","obj":"Tax:9606"},{"id":"A441","pred":"tao:has_database_id","subj":"441","obj":"Tax:694009"},{"id":"A442","pred":"tao:has_database_id","subj":"442","obj":"Tax:2697049"},{"id":"A443","pred":"tao:has_database_id","subj":"443","obj":"Tax:126910"},{"id":"A450","pred":"tao:has_database_id","subj":"450","obj":"Gene:59272"},{"id":"A451","pred":"tao:has_database_id","subj":"451","obj":"Tax:9606"},{"id":"A452","pred":"tao:has_database_id","subj":"452","obj":"Tax:694009"},{"id":"A453","pred":"tao:has_database_id","subj":"453","obj":"Tax:2697049"},{"id":"A454","pred":"tao:has_database_id","subj":"454","obj":"MESH:D054358"},{"subj":"439","pred":"source","obj":"LitCovid-PubTator"},{"subj":"440","pred":"source","obj":"LitCovid-PubTator"},{"subj":"441","pred":"source","obj":"LitCovid-PubTator"},{"subj":"442","pred":"source","obj":"LitCovid-PubTator"},{"subj":"443","pred":"source","obj":"LitCovid-PubTator"},{"subj":"450","pred":"source","obj":"LitCovid-PubTator"},{"subj":"451","pred":"source","obj":"LitCovid-PubTator"},{"subj":"452","pred":"source","obj":"LitCovid-PubTator"},{"subj":"453","pred":"source","obj":"LitCovid-PubTator"},{"subj":"454","pred":"source","obj":"LitCovid-PubTator"},{"subj":"455","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":"T199","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T200","span":{"begin":8,"end":16},"obj":"Sentence"},{"id":"T201","span":{"begin":17,"end":278},"obj":"Sentence"},{"id":"T202","span":{"begin":279,"end":401},"obj":"Sentence"},{"id":"T203","span":{"begin":402,"end":502},"obj":"Sentence"},{"id":"T204","span":{"begin":503,"end":681},"obj":"Sentence"},{"id":"T205","span":{"begin":682,"end":917},"obj":"Sentence"},{"id":"T206","span":{"begin":918,"end":1095},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T199","pred":"source","obj":"LitCovid-sentences"},{"subj":"T200","pred":"source","obj":"LitCovid-sentences"},{"subj":"T201","pred":"source","obj":"LitCovid-sentences"},{"subj":"T202","pred":"source","obj":"LitCovid-sentences"},{"subj":"T203","pred":"source","obj":"LitCovid-sentences"},{"subj":"T204","pred":"source","obj":"LitCovid-sentences"},{"subj":"T205","pred":"source","obj":"LitCovid-sentences"},{"subj":"T206","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#abec93","default":true},{"id":"LitCovid-sentences","color":"#ec93c5"}]}]}}