PMC:7441777 / 16788-18276 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T31","span":{"begin":1258,"end":1265},"obj":"Body_part"},{"id":"T32","span":{"begin":1378,"end":1385},"obj":"Body_part"}],"attributes":[{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T51","span":{"begin":187,"end":195},"obj":"Disease"}],"attributes":[{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T109","span":{"begin":100,"end":103},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"},{"id":"T110","span":{"begin":565,"end":568},"obj":"http://purl.obolibrary.org/obo/CLO_0004265"},{"id":"T111","span":{"begin":585,"end":590},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T112","span":{"begin":585,"end":590},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T247","span":{"begin":94,"end":98},"obj":"Chemical"},{"id":"T248","span":{"begin":105,"end":108},"obj":"Chemical"},{"id":"T249","span":{"begin":122,"end":132},"obj":"Chemical"},{"id":"T250","span":{"begin":134,"end":143},"obj":"Chemical"},{"id":"T252","span":{"begin":145,"end":158},"obj":"Chemical"},{"id":"T253","span":{"begin":164,"end":174},"obj":"Chemical"},{"id":"T254","span":{"begin":279,"end":281},"obj":"Chemical"},{"id":"T256","span":{"begin":501,"end":503},"obj":"Chemical"},{"id":"T258","span":{"begin":1247,"end":1257},"obj":"Chemical"},{"id":"T259","span":{"begin":1258,"end":1265},"obj":"Chemical"},{"id":"T260","span":{"begin":1378,"end":1385},"obj":"Chemical"},{"id":"T261","span":{"begin":1450,"end":1452},"obj":"Chemical"}],"attributes":[{"id":"A247","pred":"chebi_id","subj":"T247","obj":"http://purl.obolibrary.org/obo/CHEBI_4806"},{"id":"A248","pred":"chebi_id","subj":"T248","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A249","pred":"chebi_id","subj":"T249","obj":"http://purl.obolibrary.org/obo/CHEBI_28775"},{"id":"A250","pred":"chebi_id","subj":"T250","obj":"http://purl.obolibrary.org/obo/CHEBI_18152"},{"id":"A251","pred":"chebi_id","subj":"T250","obj":"http://purl.obolibrary.org/obo/CHEBI_58395"},{"id":"A252","pred":"chebi_id","subj":"T252","obj":"http://purl.obolibrary.org/obo/CHEBI_8695"},{"id":"A253","pred":"chebi_id","subj":"T253","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A254","pred":"chebi_id","subj":"T254","obj":"http://purl.obolibrary.org/obo/CHEBI_53458"},{"id":"A255","pred":"chebi_id","subj":"T254","obj":"http://purl.obolibrary.org/obo/CHEBI_74707"},{"id":"A256","pred":"chebi_id","subj":"T256","obj":"http://purl.obolibrary.org/obo/CHEBI_53458"},{"id":"A257","pred":"chebi_id","subj":"T256","obj":"http://purl.obolibrary.org/obo/CHEBI_74707"},{"id":"A258","pred":"chebi_id","subj":"T258","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A259","pred":"chebi_id","subj":"T259","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A260","pred":"chebi_id","subj":"T260","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A261","pred":"chebi_id","subj":"T261","obj":"http://purl.obolibrary.org/obo/CHEBI_53458"},{"id":"A262","pred":"chebi_id","subj":"T261","obj":"http://purl.obolibrary.org/obo/CHEBI_74707"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"383","span":{"begin":110,"end":114},"obj":"Gene"},{"id":"384","span":{"begin":198,"end":202},"obj":"Gene"},{"id":"386","span":{"begin":311,"end":314},"obj":"Gene"},{"id":"390","span":{"begin":187,"end":197},"obj":"Species"},{"id":"391","span":{"begin":164,"end":174},"obj":"Chemical"},{"id":"392","span":{"begin":504,"end":508},"obj":"Chemical"},{"id":"393","span":{"begin":1247,"end":1257},"obj":"Chemical"}],"attributes":[{"id":"A383","pred":"tao:has_database_id","subj":"383","obj":"Gene:2959"},{"id":"A384","pred":"tao:has_database_id","subj":"384","obj":"Gene:43740578"},{"id":"A386","pred":"tao:has_database_id","subj":"386","obj":"Gene:8083"},{"id":"A390","pred":"tao:has_database_id","subj":"390","obj":"Tax:2697049"},{"id":"A391","pred":"tao:has_database_id","subj":"391","obj":"MESH:C000606551"},{"id":"A392","pred":"tao:has_database_id","subj":"392","obj":"MESH:C437084"},{"id":"A393","pred":"tao:has_database_id","subj":"393","obj":"MESH:D059808"}],"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":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":100,"end":103},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T173","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T174","span":{"begin":6,"end":69},"obj":"Sentence"},{"id":"T175","span":{"begin":70,"end":496},"obj":"Sentence"},{"id":"T176","span":{"begin":497,"end":778},"obj":"Sentence"},{"id":"T177","span":{"begin":779,"end":1044},"obj":"Sentence"},{"id":"T178","span":{"begin":1045,"end":1130},"obj":"Sentence"},{"id":"T179","span":{"begin":1131,"end":1219},"obj":"Sentence"},{"id":"T180","span":{"begin":1220,"end":1488},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}

{"project":"2_test","denotations":[{"id":"32720577-31017050-56195113","span":{"begin":316,"end":320},"obj":"31017050"},{"id":"32720577-17628098-56195114","span":{"begin":341,"end":345},"obj":"17628098"},{"id":"32720577-17503456-56195115","span":{"begin":365,"end":369},"obj":"17503456"},{"id":"32720577-21595427-56195116","span":{"begin":383,"end":387},"obj":"21595427"},{"id":"32720577-23614718-56195117","span":{"begin":389,"end":393},"obj":"23614718"},{"id":"32720577-11123888-56195121","span":{"begin":453,"end":457},"obj":"11123888"},{"id":"32720577-32149220-56195122","span":{"begin":471,"end":475},"obj":"32149220"},{"id":"32720577-16458552-56195123","span":{"begin":490,"end":494},"obj":"16458552"}],"text":"2.3. Molecular mechanics Poisson-Boltzmann surface area calculations\nThe binding affinity of EGCG, TF1, TF3, TF2b, TF2a, hesperidin, myricetin, quercetagetin, and remdesivir against the SARS-CoV-2 RdRp, were calculated by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methodology (Jonniya \u0026 Kar, 2020; Kar, Seel, et al., 2007; Kar, Wei, et al., 2007; Kar et al., 2011; 2013; Kar \u0026 Knecht, 2012a, 2012b, 2012c, 2012d; Kollman et al., 2000; Roy et al., 2020; Wang et al., 2006). The MM-PBSA scheme can briefly be described as follows: (1) ΔGbind=ΔH−TΔS≈ΔEMM+ΔGsolv−TΔS (2) ΔEMM=ΔEinternal+ΔEelec+ΔEvdW (3) ΔGsolv=ΔGpol+ΔGnp where ΔEMM, ΔGsolv, TΔS are the changes in molecular mechanical energy, solvation free energy, and conformational entropy, respectively. Further, molecular mechanical energy is composed of ΔEinternal (bond, dihedral, and angle), ΔEelec (electrostatic) and ΔEvdW (van der Waals) and the change in desolvation free energy is composed of polar solvation (ΔGpol) and non-polar solvation free energy (ΔGnp). The polar solvation free energy, ΔGpol, was calculated by the pbsa module of AMBER18. Due to the high computational cost, we neglect the configurational entropy calculations. Further, to understand the polyphenol-protein interaction more closely, the interaction energy was decomposed into the contributions from each residue of the protein by using the molecular mechanics generalized Born surface area (MM-GBSA) scheme (Gohlke et al., 2003)."}