PMC:7784834 / 10992-12029 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"191","span":{"begin":505,"end":510},"obj":"Gene"}],"attributes":[{"id":"A191","pred":"tao:has_database_id","subj":"191","obj":"Gene:43740568"}],"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_"}],"text":"2.2. Determination of binding pocket and generation of receptor grid\nThe active sites enclosed in the binding pocket of spike protein and main protease were predicted using Computed Atlas of Surface Topography of proteins (CASTp) webserver (Tian et al., 2018) which calculates geometric and topological measurements of protein structures. It measures the volume and surface area of the binding pocket and also predicts the atoms involved in formation of this binding cavity. Although the active sites of spike protein and the main protease are known but still research is undergoing in which it is predicted that new amino acids might be involved in the inhibition of virus activity. In order to undertake all the possibilities, binding pocket analysis was performed through CastP. Further for the ease of molecular docking, a receptor grid was generated around the active sites of target proteins using Receptor Grid generation module. The receptor grid file was created with a grid box around the centroid of selected active residues."}

{"project":"LitCovid-sentences","denotations":[{"id":"T72","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T73","span":{"begin":6,"end":69},"obj":"Sentence"},{"id":"T74","span":{"begin":70,"end":339},"obj":"Sentence"},{"id":"T75","span":{"begin":340,"end":475},"obj":"Sentence"},{"id":"T76","span":{"begin":476,"end":684},"obj":"Sentence"},{"id":"T77","span":{"begin":685,"end":782},"obj":"Sentence"},{"id":"T78","span":{"begin":783,"end":937},"obj":"Sentence"},{"id":"T79","span":{"begin":938,"end":1037},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.2. Determination of binding pocket and generation of receptor grid\nThe active sites enclosed in the binding pocket of spike protein and main protease were predicted using Computed Atlas of Surface Topography of proteins (CASTp) webserver (Tian et al., 2018) which calculates geometric and topological measurements of protein structures. It measures the volume and surface area of the binding pocket and also predicts the atoms involved in formation of this binding cavity. Although the active sites of spike protein and the main protease are known but still research is undergoing in which it is predicted that new amino acids might be involved in the inhibition of virus activity. In order to undertake all the possibilities, binding pocket analysis was performed through CastP. Further for the ease of molecular docking, a receptor grid was generated around the active sites of target proteins using Receptor Grid generation module. The receptor grid file was created with a grid box around the centroid of selected active residues."}