{"id":"https://openalex.org/W2200865508","doi":"https://doi.org/10.1021/ci600516x","title":"Method To Assess Packing Quality of Transmembrane \u03b1-Helices in Proteins. 1. Parametrization Using Structural Data","display_name":"Method To Assess Packing Quality of Transmembrane \u03b1-Helices in Proteins. 1. Parametrization Using Structural Data","publication_year":2007,"publication_date":"2007-03-20","ids":{"openalex":"https://openalex.org/W2200865508","doi":"https://doi.org/10.1021/ci600516x","mag":"2200865508","pmid":"https://pubmed.ncbi.nlm.nih.gov/17371005"},"language":"en","primary_location":{"id":"doi:10.1021/ci600516x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci600516x","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059135046","display_name":"Anton O. Chugunov","orcid":"https://orcid.org/0000-0003-1331-3949"},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Anton O. Chugunov","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia","institution_ids":["https://openalex.org/I153845743","https://openalex.org/I19880235","https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045127480","display_name":"Valery Novoseletsky","orcid":"https://orcid.org/0000-0003-4090-4859"},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Valery N. Novoseletsky","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia","institution_ids":["https://openalex.org/I153845743","https://openalex.org/I19880235","https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059758588","display_name":"Dmitry E. Nolde","orcid":"https://orcid.org/0000-0002-3328-0024"},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitry E. Nolde","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia","institution_ids":["https://openalex.org/I153845743","https://openalex.org/I19880235","https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008332261","display_name":"Alexander S. Arseniev","orcid":"https://orcid.org/0000-0002-4986-6716"},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexander S. Arseniev","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia","institution_ids":["https://openalex.org/I153845743","https://openalex.org/I19880235","https://openalex.org/I4210105571"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000779538","display_name":"Roman G. Efremov","orcid":"https://orcid.org/0000-0002-5474-4721"},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Roman G. Efremov","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow 117997, Russia, Department of Bioengineering, Biological Faculty, M.V. Lomonosov Moscow State University, Vorobiovy gory, 119899 Moscow, Russia, and Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow Region 141700, Russia","institution_ids":["https://openalex.org/I153845743","https://openalex.org/I19880235","https://openalex.org/I4210105571"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4038,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.63853075,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"47","issue":"3","first_page":"1150","last_page":"1162"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9997000098228455,"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":0.9997000098228455,"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/T12236","display_name":"Photoreceptor and optogenetics research","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9986000061035156,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/integral-membrane-protein","display_name":"Integral membrane protein","score":0.6799607276916504},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.591713547706604},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5910381078720093},{"id":"https://openalex.org/keywords/rhodopsin","display_name":"Rhodopsin","score":0.58162522315979},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.5628268122673035},{"id":"https://openalex.org/keywords/parametrization","display_name":"Parametrization (atmospheric modeling)","score":0.5119110345840454},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.5019421577453613},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.458491712808609},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4499847888946533},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.43765637278556824},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4350450932979584},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4285624623298645},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4248321056365967},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.405366450548172},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3427111804485321},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2864081859588623},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.2146407663822174},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.19825735688209534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14443069696426392},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14006537199020386},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12528541684150696},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11092686653137207}],"concepts":[{"id":"https://openalex.org/C161200384","wikidata":"https://www.wikidata.org/wiki/Q1757382","display_name":"Integral membrane protein","level":4,"score":0.6799607276916504},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.591713547706604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5910381078720093},{"id":"https://openalex.org/C202033177","wikidata":"https://www.wikidata.org/wiki/Q423107","display_name":"Rhodopsin","level":3,"score":0.58162522315979},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.5628268122673035},{"id":"https://openalex.org/C202887219","wikidata":"https://www.wikidata.org/wiki/Q3895221","display_name":"Parametrization (atmospheric modeling)","level":3,"score":0.5119110345840454},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.5019421577453613},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.458491712808609},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4499847888946533},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.43765637278556824},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4350450932979584},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4285624623298645},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4248321056365967},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.405366450548172},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3427111804485321},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2864081859588623},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.2146407663822174},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.19825735688209534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14443069696426392},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14006537199020386},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12528541684150696},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11092686653137207},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C74902906","wikidata":"https://www.wikidata.org/wiki/Q1190858","display_name":"Radiative transfer","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C2780827179","wikidata":"https://www.wikidata.org/wiki/Q422001","display_name":"Retinal","level":2,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012243","descriptor_name":"Rhodopsin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012243","descriptor_name":"Rhodopsin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012243","descriptor_name":"Rhodopsin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci600516x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci600516x","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:17371005","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17371005","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,"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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W1963523454","https://openalex.org/W1965469554","https://openalex.org/W1969787762","https://openalex.org/W1971024387","https://openalex.org/W1971730109","https://openalex.org/W1981207136","https://openalex.org/W1991594572","https://openalex.org/W2004461664","https://openalex.org/W2008708467","https://openalex.org/W2011495938","https://openalex.org/W2013889389","https://openalex.org/W2025859600","https://openalex.org/W2033711689","https://openalex.org/W2033877477","https://openalex.org/W2034892926","https://openalex.org/W2038591618","https://openalex.org/W2041207467","https://openalex.org/W2041621703","https://openalex.org/W2048356262","https://openalex.org/W2049330624","https://openalex.org/W2057728323","https://openalex.org/W2059382484","https://openalex.org/W2063044149","https://openalex.org/W2071486470","https://openalex.org/W2074182813","https://openalex.org/W2074429985","https://openalex.org/W2076444761","https://openalex.org/W2078122870","https://openalex.org/W2078481695","https://openalex.org/W2078619116","https://openalex.org/W2081884169","https://openalex.org/W2082102819","https://openalex.org/W2084225766","https://openalex.org/W2086133094","https://openalex.org/W2088685693","https://openalex.org/W2097775366","https://openalex.org/W2098966065","https://openalex.org/W2101810621","https://openalex.org/W2106571032","https://openalex.org/W2114520383","https://openalex.org/W2115357061","https://openalex.org/W2116349394","https://openalex.org/W2119665774","https://openalex.org/W2120903461","https://openalex.org/W2130479394","https://openalex.org/W2136364519","https://openalex.org/W2137588110","https://openalex.org/W2146250729","https://openalex.org/W2147354493","https://openalex.org/W2149963584","https://openalex.org/W2151792730","https://openalex.org/W2157672388","https://openalex.org/W2158780467","https://openalex.org/W2162274915","https://openalex.org/W2163137692","https://openalex.org/W2163510478","https://openalex.org/W2170089429","https://openalex.org/W2170907233","https://openalex.org/W2171419407","https://openalex.org/W2215520647","https://openalex.org/W2618338767","https://openalex.org/W4235794372","https://openalex.org/W4246356731","https://openalex.org/W4251828057"],"related_works":["https://openalex.org/W4206949911","https://openalex.org/W3171039768","https://openalex.org/W3016550772","https://openalex.org/W2593264178","https://openalex.org/W2039679484","https://openalex.org/W2181530468","https://openalex.org/W2560155458","https://openalex.org/W3200194980","https://openalex.org/W2155159626","https://openalex.org/W2123053169"],"abstract_inverted_index":{"Integral":[0],"membrane":[1],"proteins":[2],"(MPs)":[3],"are":[4],"pharmaceutical":[5],"targets":[6],"of":[7,12,25,53,60,70,81,85,99,112,130,144,162,170,176,184,193,211,214],"exceptional":[8],"importance.":[9],"Modern":[10],"methods":[11,55],"three-dimensional":[13],"protein":[14,100],"structure":[15,169],"determination":[16],"often":[17],"fail":[18],"to":[19,78,118,140,165],"supply":[20],"the":[21,30,48,57,61,79,82,97,119,122,137,150,163,167,185,190,199],"fast":[22],"growing":[23],"field":[24],"structure-based":[26],"drug":[27],"design":[28],"with":[29],"requested":[31],"MPs'":[32,62],"structures.":[33],"That":[34],"is":[35,56,94,108,187],"why":[36],"computational":[37,76],"modeling":[38],"techniques":[39],"gain":[40],"a":[41,75,127,174],"special":[42],"importance":[43],"for":[44],"these":[45,54],"objects.":[46],"Among":[47],"principal":[49],"difficulties":[50],"limiting":[51],"application":[52],"low":[58],"quality":[59],"models":[63,210],"built":[64],"in":[65,90,110,189,207],"silico.":[66],"In":[67,121],"this":[68,194],"series":[69],"two":[71],"papers":[72],"we":[73,125,148],"present":[74],"approach":[77,152],"assessment":[80],"packing":[83],"\"quality\"":[84],"transmembrane":[86],"(TM)":[87],"alpha-helical":[88,133],"domains":[89,134,213],"proteins.":[91],"The":[92],"method":[93,164,186,203],"based":[95],"on":[96],"concept":[98],"environment":[101,114],"classes,":[102],"whereby":[103],"each":[104],"amino":[105],"acid":[106],"residue":[107],"described":[109],"terms":[111],"its":[113,177],"polarity":[115],"and":[116,135,160,173],"accessibility":[117],"membrane.":[120],"first":[123],"paper":[124],"analyze":[126],"nonredundant":[128],"set":[129],"26":[131],"TM":[132,212],"compute":[136],"residues'":[138],"propensities":[139],"five":[141],"predefined":[142],"classes":[143],"membrane-protein":[145],"environments.":[146],"Here":[147],"evaluate":[149],"proposed":[151],"only":[153],"by":[154],"various":[155],"test":[156],"sets,":[157],"cross-validation":[158],"protocols":[159],"ability":[161],"delimit":[166],"crystal":[168],"visual":[171],"rhodopsin,":[172],"number":[175],"erroneous":[178],"theoretical":[179],"models.":[180],"More":[181],"advanced":[182],"validation":[183],"given":[188],"second":[191],"article":[192],"series.":[195],"We":[196],"assume":[197],"that":[198],"developed":[200],"\"membrane":[201],"score\"":[202],"will":[204],"be":[205],"helpful":[206],"optimizing":[208],"computer":[209],"MPs,":[215],"especially":[216],"G-protein":[217],"coupled":[218],"receptors.":[219]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2016-06-24T00:00:00"}