PMC:7643666 / 7483-8448 JSONTXT

{"project":"Zoonoses","denotations":[{"id":"T20","span":{"begin":285,"end":288},"obj":"Phenomena"}],"attributes":[{"id":"A20","pred":"tao:has_database_id","subj":"T20","obj":"MESH:D000072417"}],"text":"2.2 Molecular docking\nMolecular docking was performed using HDOCK server (http://hdock.phys.hust.edu.cn/), which calculates protein-protein interaction through a hybrid algorithm of template-based and template-free docking. The crystal structure of S protein receptor binding domain (RBD) (PDB ID: 6M0J), corresponding to the residues 437–508 of S protein, was docked against the homology models of bat ACE2 [27]. The calculation was carried out imposing as constraints 8 Å distance between S protein A475 and ACE2 E23 and 5 Å distance between S protein N501 and ACE2 D355. The results were analyzed according to i) docking score value (kcal/mol), generated by HDOCK scoring function [28]; ii) ligand root-mean-square deviation (RMSD) of atomic positions value (Å). RMSD measures the distance between the docked pose and a model of the same ligand predicted by template-based homology modelling generated by HDOCK (the lower the value, the more similar the poses)."}

{"project":"Covid19_manual_annotation_v2","denotations":[{"id":"T20","span":{"begin":285,"end":288},"obj":"Phenomena"}],"attributes":[{"id":"A20","pred":"tao:has_database_id","subj":"T20","obj":"MESH:D000072417"}],"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":"BioProject","uri":"https://www.ncbi.nlm.nih.gov/bioproject/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"},{"prefix":"HP","uri":"https://hpo.jax.org/app/browse/term/HP:"},{"prefix":"BioSample","uri":"https://www.ncbi.nlm.nih.gov/biosample/"}],"text":"2.2 Molecular docking\nMolecular docking was performed using HDOCK server (http://hdock.phys.hust.edu.cn/), which calculates protein-protein interaction through a hybrid algorithm of template-based and template-free docking. The crystal structure of S protein receptor binding domain (RBD) (PDB ID: 6M0J), corresponding to the residues 437–508 of S protein, was docked against the homology models of bat ACE2 [27]. The calculation was carried out imposing as constraints 8 Å distance between S protein A475 and ACE2 E23 and 5 Å distance between S protein N501 and ACE2 D355. The results were analyzed according to i) docking score value (kcal/mol), generated by HDOCK scoring function [28]; ii) ligand root-mean-square deviation (RMSD) of atomic positions value (Å). RMSD measures the distance between the docked pose and a model of the same ligand predicted by template-based homology modelling generated by HDOCK (the lower the value, the more similar the poses)."}