{"id":"https://openalex.org/W2105899060","doi":"https://doi.org/10.1093/bioinformatics/bts233","title":"Ranking models of transmembrane <i>\u03b2</i>-barrel proteins using Z-coordinate predictions","display_name":"Ranking models of transmembrane <i>\u03b2</i>-barrel proteins using Z-coordinate predictions","publication_year":2012,"publication_date":"2012-06-09","ids":{"openalex":"https://openalex.org/W2105899060","doi":"https://doi.org/10.1093/bioinformatics/bts233","mag":"2105899060","pmid":"https://pubmed.ncbi.nlm.nih.gov/22689784"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i90/48874506/bioinformatics_28_12_i90.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i90/48874506/bioinformatics_28_12_i90.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041018040","display_name":"Sikander Hayat","orcid":"https://orcid.org/0000-0001-5919-8371"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Sikander Hayat","raw_affiliation_strings":["Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072903725","display_name":"Arne Elofsson","orcid":"https://orcid.org/0000-0002-7115-9751"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Arne Elofsson","raw_affiliation_strings":["Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041018040"],"corresponding_institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9412,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.74226595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"12","first_page":"i90","last_page":"i96"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991000294685364,"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":0.9987000226974487,"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/transmembrane-protein","display_name":"Transmembrane protein","score":0.6640934944152832},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5684162378311157},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5248936414718628},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5057127475738525},{"id":"https://openalex.org/keywords/coordinate-system","display_name":"Coordinate system","score":0.46493834257125854},{"id":"https://openalex.org/keywords/barrel","display_name":"Barrel (horology)","score":0.445990651845932},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.44242265820503235},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35507771372795105},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35331881046295166},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3420186936855316},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29869091510772705},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24903112649917603},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23149901628494263},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.15351632237434387},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1506199836730957},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10965648293495178},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10920453071594238},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.09842294454574585}],"concepts":[{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.6640934944152832},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5684162378311157},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5248936414718628},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5057127475738525},{"id":"https://openalex.org/C80551277","wikidata":"https://www.wikidata.org/wiki/Q11210","display_name":"Coordinate system","level":2,"score":0.46493834257125854},{"id":"https://openalex.org/C172227984","wikidata":"https://www.wikidata.org/wiki/Q1400397","display_name":"Barrel (horology)","level":2,"score":0.445990651845932},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.44242265820503235},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35507771372795105},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35331881046295166},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3420186936855316},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29869091510772705},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24903112649917603},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23149901628494263},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.15351632237434387},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1506199836730957},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10965648293495178},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10920453071594238},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.09842294454574585},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","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":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i90/48874506/bioinformatics_28_12_i90.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22689784","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22689784","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:DiVA.org:su-80010","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-80010","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:europepmc.org:2378085","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3371865","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts233","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts233","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i90/48874506/bioinformatics_28_12_i90.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1999808683","display_name":null,"funder_award_id":"VR-NT 2009-5072","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G4227476342","display_name":null,"funder_award_id":"VR-NT","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8334154220","display_name":null,"funder_award_id":"2010-3555","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8383890082","display_name":null,"funder_award_id":"VR-M 2010-3555","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320338377","display_name":"FP7 Health","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2105899060.pdf","grobid_xml":"https://content.openalex.org/works/W2105899060.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1821139715","https://openalex.org/W1967513793","https://openalex.org/W1974473654","https://openalex.org/W1976179956","https://openalex.org/W1985225270","https://openalex.org/W1987438054","https://openalex.org/W1999612183","https://openalex.org/W2001808731","https://openalex.org/W2004691211","https://openalex.org/W2004696942","https://openalex.org/W2006600449","https://openalex.org/W2012534599","https://openalex.org/W2020411123","https://openalex.org/W2049357350","https://openalex.org/W2052595824","https://openalex.org/W2085212975","https://openalex.org/W2097775366","https://openalex.org/W2108564508","https://openalex.org/W2117815535","https://openalex.org/W2119587675","https://openalex.org/W2121725953","https://openalex.org/W2128361588","https://openalex.org/W2137095432","https://openalex.org/W2137382456","https://openalex.org/W2137670821","https://openalex.org/W2138217546","https://openalex.org/W2143059772","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2166618626","https://openalex.org/W2167393453","https://openalex.org/W2167512705"],"related_works":["https://openalex.org/W3099772455","https://openalex.org/W3172198228","https://openalex.org/W1986078734","https://openalex.org/W2129301794","https://openalex.org/W1540599686","https://openalex.org/W2016396528","https://openalex.org/W4377101717","https://openalex.org/W2261012589","https://openalex.org/W1925092754","https://openalex.org/W2045836921"],"abstract_inverted_index":{"Tobmodel":[0],"is":[1],"freely":[2],"available":[3,19],"as":[4],"a":[5],"web":[6],"server":[7],"at:":[8],"http://tobmodel.cbr.su.se/.":[9],"The":[10],"datasets":[11],"used":[12],"for":[13],"training":[14],"and":[15],"evaluations":[16],"are":[17],"also":[18],"from":[20],"this":[21],"site.":[22]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
