PMC:7081066 / 5161-5975 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"159","span":{"begin":57,"end":61},"obj":"Gene"},{"id":"160","span":{"begin":333,"end":337},"obj":"Gene"},{"id":"161","span":{"begin":472,"end":477},"obj":"Gene"},{"id":"162","span":{"begin":501,"end":505},"obj":"Gene"},{"id":"163","span":{"begin":323,"end":328},"obj":"Gene"},{"id":"164","span":{"begin":162,"end":167},"obj":"Gene"},{"id":"165","span":{"begin":31,"end":36},"obj":"Gene"},{"id":"166","span":{"begin":22,"end":30},"obj":"Species"},{"id":"167","span":{"begin":151,"end":161},"obj":"Species"}],"attributes":[{"id":"A159","pred":"tao:has_database_id","subj":"159","obj":"Gene:59272"},{"id":"A160","pred":"tao:has_database_id","subj":"160","obj":"Gene:59272"},{"id":"A161","pred":"tao:has_database_id","subj":"161","obj":"Gene:43740568"},{"id":"A162","pred":"tao:has_database_id","subj":"162","obj":"Gene:59272"},{"id":"A163","pred":"tao:has_database_id","subj":"163","obj":"Gene:43740568"},{"id":"A164","pred":"tao:has_database_id","subj":"164","obj":"Gene:43740568"},{"id":"A165","pred":"tao:has_database_id","subj":"165","obj":"Gene:43740568"},{"id":"A166","pred":"tao:has_database_id","subj":"166","obj":"Tax:694009"},{"id":"A167","pred":"tao:has_database_id","subj":"167","obj":"Tax:2697049"}],"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":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T32","span":{"begin":103,"end":110},"obj":"Body_part"},{"id":"T33","span":{"begin":181,"end":188},"obj":"Body_part"},{"id":"T34","span":{"begin":478,"end":485},"obj":"Body_part"}],"attributes":[{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T24","span":{"begin":22,"end":30},"obj":"Disease"},{"id":"T25","span":{"begin":151,"end":159},"obj":"Disease"}],"attributes":[{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T32","span":{"begin":440,"end":441},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T33","span":{"begin":564,"end":566},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T37","span":{"begin":103,"end":110},"obj":"Chemical"},{"id":"T38","span":{"begin":181,"end":188},"obj":"Chemical"},{"id":"T39","span":{"begin":464,"end":470},"obj":"Chemical"},{"id":"T40","span":{"begin":478,"end":485},"obj":"Chemical"}],"attributes":[{"id":"A37","pred":"chebi_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/CHEBI_16541"},{"id":"A38","pred":"chebi_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/CHEBI_16541"},{"id":"A39","pred":"chebi_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A40","pred":"chebi_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"LitCovid-sentences","denotations":[{"id":"T45","span":{"begin":0,"end":121},"obj":"Sentence"},{"id":"T46","span":{"begin":122,"end":180},"obj":"Sentence"},{"id":"T47","span":{"begin":181,"end":236},"obj":"Sentence"},{"id":"T48","span":{"begin":237,"end":386},"obj":"Sentence"},{"id":"T49","span":{"begin":387,"end":569},"obj":"Sentence"},{"id":"T50","span":{"begin":570,"end":693},"obj":"Sentence"},{"id":"T51","span":{"begin":694,"end":814},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"MyTest","denotations":[{"id":"32210742-24532726-29811233","span":{"begin":564,"end":566},"obj":"24532726"},{"id":"32210742-27503228-29811234","span":{"begin":688,"end":690},"obj":"27503228"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

{"project":"2_test","denotations":[{"id":"32210742-24532726-29811233","span":{"begin":564,"end":566},"obj":"24532726"},{"id":"32210742-27503228-29811234","span":{"begin":688,"end":690},"obj":"27503228"}],"text":"Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}