PMC:7594251 / 94313-95568 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T197","span":{"begin":175,"end":182},"obj":"Body_part"},{"id":"T198","span":{"begin":252,"end":262},"obj":"Body_part"},{"id":"T199","span":{"begin":347,"end":357},"obj":"Body_part"},{"id":"T200","span":{"begin":433,"end":440},"obj":"Body_part"},{"id":"T201","span":{"begin":483,"end":490},"obj":"Body_part"},{"id":"T202","span":{"begin":748,"end":759},"obj":"Body_part"},{"id":"T203","span":{"begin":944,"end":955},"obj":"Body_part"}],"attributes":[{"id":"A197","pred":"fma_id","subj":"T197","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A198","pred":"fma_id","subj":"T198","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A199","pred":"fma_id","subj":"T199","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A200","pred":"fma_id","subj":"T200","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A201","pred":"fma_id","subj":"T201","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A202","pred":"fma_id","subj":"T202","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A203","pred":"fma_id","subj":"T203","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"A third method called structural information using Overhauser effects and selective labeling (SOS-NMR), relies of STD experiments performed on ligand complexes with different protein samples that have been fully deuterated excluding a specific type of amino acid. In other words, the data obtained by SOS-NMR gives insight into the ligand-binding amino acid composition and when taken into consideration the 3D structure of targeted protein can be used to establish the structure of protein-ligand complex. This approach has been demonstrated using two complexes—FKBP complexed to 2-(3′-pyridyl)-benzimidazole and MurA complexed to uridine diphosphateN-acetylglucosamine (UDP-GlcNAc). The results showed that for FKBP and MurA, only four and three amino acids (FKBP: Ile, Val, Leu, Met; MurA: Trp, Phe, His) were needed to be selectively protonated in perdeuterated samples to establish the ligand-binding site. Additionally, on average only 6 amino acids were required for accurate identification of ligand-binding surface. According to authors SOS-NMR can greatly improve the early stages of the drug discovery process [397]. Moreover, combining SOS-NMR with other methods can even further increase chances for a positive outcome of an experiment [398]."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T107","span":{"begin":94,"end":97},"obj":"Disease"},{"id":"T108","span":{"begin":114,"end":117},"obj":"Disease"},{"id":"T109","span":{"begin":301,"end":304},"obj":"Disease"},{"id":"T110","span":{"begin":1046,"end":1049},"obj":"Disease"},{"id":"T111","span":{"begin":1148,"end":1151},"obj":"Disease"}],"attributes":[{"id":"A107","pred":"mondo_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/MONDO_0011604"},{"id":"A108","pred":"mondo_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/MONDO_0021681"},{"id":"A109","pred":"mondo_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/MONDO_0011604"},{"id":"A110","pred":"mondo_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/MONDO_0011604"},{"id":"A111","pred":"mondo_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/MONDO_0011604"}],"text":"A third method called structural information using Overhauser effects and selective labeling (SOS-NMR), relies of STD experiments performed on ligand complexes with different protein samples that have been fully deuterated excluding a specific type of amino acid. In other words, the data obtained by SOS-NMR gives insight into the ligand-binding amino acid composition and when taken into consideration the 3D structure of targeted protein can be used to establish the structure of protein-ligand complex. This approach has been demonstrated using two complexes—FKBP complexed to 2-(3′-pyridyl)-benzimidazole and MurA complexed to uridine diphosphateN-acetylglucosamine (UDP-GlcNAc). The results showed that for FKBP and MurA, only four and three amino acids (FKBP: Ile, Val, Leu, Met; MurA: Trp, Phe, His) were needed to be selectively protonated in perdeuterated samples to establish the ligand-binding site. Additionally, on average only 6 amino acids were required for accurate identification of ligand-binding surface. According to authors SOS-NMR can greatly improve the early stages of the drug discovery process [397]. Moreover, combining SOS-NMR with other methods can even further increase chances for a positive outcome of an experiment [398]."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T665","span":{"begin":0,"end":1},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T666","span":{"begin":84,"end":92},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"},{"id":"T667","span":{"begin":233,"end":234},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T668","span":{"begin":521,"end":524},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T669","span":{"begin":772,"end":775},"obj":"http://purl.obolibrary.org/obo/CLO_0037067"},{"id":"T670","span":{"begin":1213,"end":1214},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"A third method called structural information using Overhauser effects and selective labeling (SOS-NMR), relies of STD experiments performed on ligand complexes with different protein samples that have been fully deuterated excluding a specific type of amino acid. In other words, the data obtained by SOS-NMR gives insight into the ligand-binding amino acid composition and when taken into consideration the 3D structure of targeted protein can be used to establish the structure of protein-ligand complex. This approach has been demonstrated using two complexes—FKBP complexed to 2-(3′-pyridyl)-benzimidazole and MurA complexed to uridine diphosphateN-acetylglucosamine (UDP-GlcNAc). The results showed that for FKBP and MurA, only four and three amino acids (FKBP: Ile, Val, Leu, Met; MurA: Trp, Phe, His) were needed to be selectively protonated in perdeuterated samples to establish the ligand-binding site. Additionally, on average only 6 amino acids were required for accurate identification of ligand-binding surface. According to authors SOS-NMR can greatly improve the early stages of the drug discovery process [397]. Moreover, combining SOS-NMR with other methods can even further increase chances for a positive outcome of an experiment [398]."}

LitCovid-PD-CHEBI

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"979","span":{"begin":581,"end":609},"obj":"Chemical"},{"id":"980","span":{"begin":632,"end":670},"obj":"Chemical"},{"id":"981","span":{"begin":672,"end":682},"obj":"Chemical"},{"id":"982","span":{"begin":767,"end":770},"obj":"Chemical"},{"id":"983","span":{"begin":772,"end":775},"obj":"Chemical"},{"id":"984","span":{"begin":777,"end":780},"obj":"Chemical"},{"id":"985","span":{"begin":793,"end":796},"obj":"Chemical"},{"id":"986","span":{"begin":798,"end":801},"obj":"Chemical"},{"id":"987","span":{"begin":803,"end":806},"obj":"Chemical"}],"attributes":[{"id":"A982","pred":"tao:has_database_id","subj":"982","obj":"MESH:D007532"},{"id":"A983","pred":"tao:has_database_id","subj":"983","obj":"MESH:D014633"},{"id":"A984","pred":"tao:has_database_id","subj":"984","obj":"MESH:D007930"},{"id":"A985","pred":"tao:has_database_id","subj":"985","obj":"MESH:D014364"},{"id":"A986","pred":"tao:has_database_id","subj":"986","obj":"MESH:D010649"},{"id":"A987","pred":"tao:has_database_id","subj":"987","obj":"MESH:D006639"}],"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":"A third method called structural information using Overhauser effects and selective labeling (SOS-NMR), relies of STD experiments performed on ligand complexes with different protein samples that have been fully deuterated excluding a specific type of amino acid. In other words, the data obtained by SOS-NMR gives insight into the ligand-binding amino acid composition and when taken into consideration the 3D structure of targeted protein can be used to establish the structure of protein-ligand complex. This approach has been demonstrated using two complexes—FKBP complexed to 2-(3′-pyridyl)-benzimidazole and MurA complexed to uridine diphosphateN-acetylglucosamine (UDP-GlcNAc). The results showed that for FKBP and MurA, only four and three amino acids (FKBP: Ile, Val, Leu, Met; MurA: Trp, Phe, His) were needed to be selectively protonated in perdeuterated samples to establish the ligand-binding site. Additionally, on average only 6 amino acids were required for accurate identification of ligand-binding surface. According to authors SOS-NMR can greatly improve the early stages of the drug discovery process [397]. Moreover, combining SOS-NMR with other methods can even further increase chances for a positive outcome of an experiment [398]."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T614","span":{"begin":0,"end":263},"obj":"Sentence"},{"id":"T615","span":{"begin":264,"end":506},"obj":"Sentence"},{"id":"T616","span":{"begin":507,"end":684},"obj":"Sentence"},{"id":"T617","span":{"begin":685,"end":766},"obj":"Sentence"},{"id":"T618","span":{"begin":767,"end":792},"obj":"Sentence"},{"id":"T619","span":{"begin":793,"end":911},"obj":"Sentence"},{"id":"T620","span":{"begin":912,"end":1024},"obj":"Sentence"},{"id":"T621","span":{"begin":1025,"end":1127},"obj":"Sentence"},{"id":"T622","span":{"begin":1128,"end":1255},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A third method called structural information using Overhauser effects and selective labeling (SOS-NMR), relies of STD experiments performed on ligand complexes with different protein samples that have been fully deuterated excluding a specific type of amino acid. In other words, the data obtained by SOS-NMR gives insight into the ligand-binding amino acid composition and when taken into consideration the 3D structure of targeted protein can be used to establish the structure of protein-ligand complex. This approach has been demonstrated using two complexes—FKBP complexed to 2-(3′-pyridyl)-benzimidazole and MurA complexed to uridine diphosphateN-acetylglucosamine (UDP-GlcNAc). The results showed that for FKBP and MurA, only four and three amino acids (FKBP: Ile, Val, Leu, Met; MurA: Trp, Phe, His) were needed to be selectively protonated in perdeuterated samples to establish the ligand-binding site. Additionally, on average only 6 amino acids were required for accurate identification of ligand-binding surface. According to authors SOS-NMR can greatly improve the early stages of the drug discovery process [397]. Moreover, combining SOS-NMR with other methods can even further increase chances for a positive outcome of an experiment [398]."}