PMC:7594251 / 102107-103373 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T15","span":{"begin":89,"end":96},"obj":"Body_part"},{"id":"T16","span":{"begin":177,"end":195},"obj":"Body_part"},{"id":"T17","span":{"begin":238,"end":245},"obj":"Body_part"},{"id":"T18","span":{"begin":328,"end":335},"obj":"Body_part"},{"id":"T19","span":{"begin":616,"end":622},"obj":"Body_part"}],"attributes":[{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma67906"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma82764"}],"text":"3.6.9. SAMPLEX\nAnother program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes. SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state. The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state). This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2. The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state. To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction. For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state. That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T118","span":{"begin":48,"end":51},"obj":"Disease"}],"attributes":[{"id":"A118","pred":"mondo_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/MONDO_0005078"}],"text":"3.6.9. SAMPLEX\nAnother program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes. SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state. The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state). This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2. The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state. To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction. For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state. That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T21","span":{"begin":109,"end":117},"obj":"http://www.ebi.ac.uk/efo/EFO_0000876"},{"id":"T22","span":{"begin":177,"end":195},"obj":"http://purl.obolibrary.org/obo/GO_0043234"},{"id":"T23","span":{"begin":326,"end":327},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T24","span":{"begin":376,"end":377},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T25","span":{"begin":421,"end":422},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T26","span":{"begin":472,"end":473},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T27","span":{"begin":557,"end":563},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T28","span":{"begin":1040,"end":1043},"obj":"http://purl.obolibrary.org/obo/CLO_0001195"}],"text":"3.6.9. SAMPLEX\nAnother program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes. SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state. The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state). This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2. The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state. To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction. For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state. That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T79552","span":{"begin":89,"end":96},"obj":"Chemical"},{"id":"T41635","span":{"begin":177,"end":185},"obj":"Chemical"},{"id":"T4092","span":{"begin":238,"end":245},"obj":"Chemical"},{"id":"T35786","span":{"begin":328,"end":335},"obj":"Chemical"},{"id":"T89568","span":{"begin":616,"end":622},"obj":"Chemical"},{"id":"T81502","span":{"begin":652,"end":661},"obj":"Chemical"},{"id":"T93491","span":{"begin":662,"end":684},"obj":"Chemical"},{"id":"T66488","span":{"begin":675,"end":684},"obj":"Chemical"},{"id":"T88221","span":{"begin":745,"end":767},"obj":"Chemical"},{"id":"T34199","span":{"begin":758,"end":767},"obj":"Chemical"}],"attributes":[{"id":"A2931","pred":"chebi_id","subj":"T79552","obj":"http://purl.obolibrary.org/obo/CHEBI_16541"},{"id":"A29114","pred":"chebi_id","subj":"T41635","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A59645","pred":"chebi_id","subj":"T4092","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A21240","pred":"chebi_id","subj":"T35786","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A34215","pred":"chebi_id","subj":"T89568","obj":"http://purl.obolibrary.org/obo/CHEBI_17822"},{"id":"A90201","pred":"chebi_id","subj":"T81502","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A795","pred":"chebi_id","subj":"T93491","obj":"http://purl.obolibrary.org/obo/CHEBI_64943"},{"id":"A34319","pred":"chebi_id","subj":"T66488","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A4458","pred":"chebi_id","subj":"T88221","obj":"http://purl.obolibrary.org/obo/CHEBI_64943"},{"id":"A64284","pred":"chebi_id","subj":"T34199","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"}],"text":"3.6.9. SAMPLEX\nAnother program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes. SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state. The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state). This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2. The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state. To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction. For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state. That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1111","span":{"begin":616,"end":622},"obj":"Chemical"}],"attributes":[{"id":"A1111","pred":"tao:has_database_id","subj":"1111","obj":"MESH:D012694"}],"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":"3.6.9. SAMPLEX\nAnother program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes. SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state. The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state). This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2. The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state. To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction. For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state. That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T674","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T675","span":{"begin":7,"end":14},"obj":"Sentence"},{"id":"T676","span":{"begin":15,"end":196},"obj":"Sentence"},{"id":"T677","span":{"begin":197,"end":354},"obj":"Sentence"},{"id":"T678","span":{"begin":355,"end":538},"obj":"Sentence"},{"id":"T679","span":{"begin":539,"end":687},"obj":"Sentence"},{"id":"T680","span":{"begin":688,"end":826},"obj":"Sentence"},{"id":"T681","span":{"begin":827,"end":933},"obj":"Sentence"},{"id":"T682","span":{"begin":934,"end":1110},"obj":"Sentence"},{"id":"T683","span":{"begin":1111,"end":1266},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.6.9. SAMPLEX\nAnother program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes. SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state. The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state). This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2. The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state. To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction. For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state. That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408]."}