PMC:7784834 / 15927-17006
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7784834","sourcedb":"PMC","sourceid":"7784834","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7784834","text":"Various analyses were performed with the help of inbuilt analysis commands of GROMACS. The root mean square deviation (RMSD) is a magnitude of the dimensional disparity among the two stagnant structures, and RMSD calculation is achieved depending upon the native structure and each consecutive trajectory frames in the simulation. In addition, root mean square fluctuation (RMSF) profile measures the affability of every protein residue depending on the fluctuation about an average location within all MD simulations (Knapp et al., 2011). Therefore, RMSD and RMSF of each simulation system were determined to examine the stability and residual fluctuations. Further, the radius of gyration (Rg) analysis was performed to evaluate the compactness of both the simulation systems separately. Also, the hydrogen bond analysis was performed to check the neighboring interactions with both simulation systems separately, including the hydrophobic interactions with the help of the LigPlot tool for both spike protein and main protease complexes with rutin before and after simulation.","tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"226","span":{"begin":998,"end":1003},"obj":"Gene"},{"id":"227","span":{"begin":800,"end":808},"obj":"Chemical"}],"attributes":[{"id":"A226","pred":"tao:has_database_id","subj":"226","obj":"Gene:43740568"},{"id":"A227","pred":"tao:has_database_id","subj":"227","obj":"MESH:D006859"},{"subj":"226","pred":"source","obj":"LitCovid-PubTator"},{"subj":"227","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":"T107","span":{"begin":0,"end":86},"obj":"Sentence"},{"id":"T108","span":{"begin":87,"end":330},"obj":"Sentence"},{"id":"T109","span":{"begin":331,"end":539},"obj":"Sentence"},{"id":"T110","span":{"begin":540,"end":658},"obj":"Sentence"},{"id":"T111","span":{"begin":659,"end":789},"obj":"Sentence"},{"id":"T112","span":{"begin":790,"end":1079},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T107","pred":"source","obj":"LitCovid-sentences"},{"subj":"T108","pred":"source","obj":"LitCovid-sentences"},{"subj":"T109","pred":"source","obj":"LitCovid-sentences"},{"subj":"T110","pred":"source","obj":"LitCovid-sentences"},{"subj":"T111","pred":"source","obj":"LitCovid-sentences"},{"subj":"T112","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#93ecb5","default":true},{"id":"LitCovid-sentences","color":"#ec9b93"}]}]}}