{"id":"https://openalex.org/W2007148127","doi":"https://doi.org/10.1073/pnas.1107702108","title":"Difference between restoring and predicting 3D structures of the loops in G-protein\u2013coupled receptors by molecular modeling","display_name":"Difference between restoring and predicting 3D structures of the loops in G-protein\u2013coupled receptors by molecular modeling","publication_year":2011,"publication_date":"2011-07-01","ids":{"openalex":"https://openalex.org/W2007148127","doi":"https://doi.org/10.1073/pnas.1107702108","mag":"2007148127","pmid":"https://pubmed.ncbi.nlm.nih.gov/21724986","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3145683"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.1107702108","doi":"https://doi.org/10.1073/pnas.1107702108","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.1107702108","pdf_url":"https://www.pnas.org/content/pnas/108/30/E341.full.pdf","source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"volume":null,"type":"letter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://www.pnas.org/content/pnas/108/30/E341.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061557305","display_name":"Gregory V. Nikiforovich","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gregory V. Nikiforovich","raw_affiliation_strings":["MolLife Design LLC, St. Louis, MO 63141; and Departments of"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MolLife Design LLC, St. Louis, MO 63141; and Departments of","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Christina M. Taylor","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christina M. Taylor","raw_affiliation_strings":["Biochemistry and Molecular Biophysics and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemistry and Molecular Biophysics and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007617580","display_name":"Garland R. Marshall","orcid":"https://orcid.org/0000-0002-3098-0332","observed_orcids":["https://orcid.org/0000-0002-3098-0332"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Garland R. Marshall","raw_affiliation_strings":["Biochemistry and Molecular Biophysics and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biochemistry and Molecular Biophysics and","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081155797","display_name":"Thomas Baranski","orcid":"https://orcid.org/0000-0002-4699-5192","observed_orcids":["https://orcid.org/0000-0002-4699-5192"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas J. Baranski","raw_affiliation_strings":["Internal Medicine, Washington University Medical School, St. Louis, MO 63110"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Internal Medicine, Washington University Medical School, St. Louis, MO 63110","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"108","issue":"30","first_page":"E341; author reply E342","last_page":"E341; author reply E342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.8413000106811523,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.8413000106811523,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.14730000495910645,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.00570000009611249,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/g-protein-coupled-receptors","display_name":"G protein-coupled receptors","score":0.9929999709129333},{"id":"https://openalex.org/keywords/3d-structure-prediction","display_name":"3D structure prediction","score":0.8889999985694885},{"id":"https://openalex.org/keywords/molecular-modeling","display_name":"molecular modeling","score":0.6570000052452087},{"id":"https://openalex.org/keywords/structure-activity-relationship","display_name":"structure-activity relationship","score":0.3919999897480011}],"concepts":[{"id":"https://openalex.org/C202033177","wikidata":"https://www.wikidata.org/wiki/Q423107","display_name":"Rhodopsin","level":3,"score":0.8054121136665344},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.6765894293785095},{"id":"https://openalex.org/C28406088","wikidata":"https://www.wikidata.org/wiki/Q5571762","display_name":"Extracellular","level":2,"score":0.5995978116989136},{"id":"https://openalex.org/C135285700","wikidata":"https://www.wikidata.org/wiki/Q38173","display_name":"G protein-coupled receptor","level":3,"score":0.4662109315395355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40655410289764404},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4043709933757782},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3530728816986084},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3341587781906128},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.24591100215911865},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1968860626220703},{"id":"https://openalex.org/C2780827179","wikidata":"https://www.wikidata.org/wiki/Q422001","display_name":"Retinal","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1073/pnas.1107702108","doi":"https://doi.org/10.1073/pnas.1107702108","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.1107702108","pdf_url":"https://www.pnas.org/content/pnas/108/30/E341.full.pdf","source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3145683","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3145683","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proc Natl Acad Sci U S A","raw_type":"Text"},{"id":"pmid:21724986","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21724986","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":"Comment"}],"best_oa_location":{"id":"doi:10.1073/pnas.1107702108","doi":"https://doi.org/10.1073/pnas.1107702108","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.1107702108","pdf_url":"https://www.pnas.org/content/pnas/108/30/E341.full.pdf","source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2007148127.pdf","grobid_xml":"https://content.openalex.org/works/W2007148127.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W2070557084","https://openalex.org/W2151784842"],"related_works":["https://openalex.org/W2151784842","https://openalex.org/W2070557084","https://openalex.org/W2044853688","https://openalex.org/W2413393553","https://openalex.org/W2016140206","https://openalex.org/W2945066357","https://openalex.org/W2053644606","https://openalex.org/W2103124460","https://openalex.org/W2074213957","https://openalex.org/W142246363"],"abstract_inverted_index":{"Goldfeld":[0,78,132],"et":[1,79,133],"al.":[2,80,134],"(1)":[3,81],"presented":[4],"modeling":[5,76,122],"results":[6],"on":[7],"restoring":[8],"3D":[9],"structures":[10,49,90],"of":[11,42,71,86,91,106],"the":[12,38,43,46,58,69,88,92,107,120],"intra-":[13],"and":[14,30],"extracellular":[15,55],"loops":[16,44,56,108],"in":[17,63,97],"bovine":[18],"rhodopsin":[19],"(bRh),":[20],"human":[21,31],"A2A":[22],"adenosine":[23],"receptor":[24,28,33],"(A2Ar),":[25],"turkey":[26],"\u03b21-adrenergic":[27],"(\u03b21AR),":[29],"\u03b22-adrenergic":[32],"(\u03b22AR).":[34],"In":[35],"all":[36],"cases,":[37],"lowest":[39],"energy":[40],"conformers":[41],"matched":[45],"corresponding":[47],"X-ray":[48,89],"with":[50,68,101],"excellent":[51],"rmsd":[52],"values.":[53],"The":[54],"for":[57],"same":[59],"receptors":[60],"were":[61,127],"modeled":[62],"our":[64],"article":[65],"previously":[66],"(2)":[67],"use":[70],"a":[72],"much":[73],"less":[74],"sophisticated":[75],"procedure.":[77],"emphasized":[82],"substantially":[83],"better":[84],"accuracy":[85],"reproducing":[87],"loops,":[93,96],"especially":[94],"larger":[95],"their":[98,104],"study":[99],"compared":[100],"ours.":[102],"Although":[103],"restoration":[105],"is":[109,114],"impressive,":[110],"we":[111],"believe":[112],"it":[113],"important":[115],"to":[116],"outline":[117],"differences":[118],"between":[119],"two":[121],"procedures":[123],"(1,":[124],"2)":[125],"that":[126],"not":[128],"sufficiently":[129],"distinguished":[130],"by":[131],"(1).":[135]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2016-06-24T00:00:00"}