{"id":"https://openalex.org/W4384663444","doi":"https://doi.org/10.1002/prot.26552","title":"Outer membrane \u03b2\u2010barrel structure prediction through the lens of AlphaFold2","display_name":"Outer membrane \u03b2\u2010barrel structure prediction through the lens of AlphaFold2","publication_year":2023,"publication_date":"2023-07-19","ids":{"openalex":"https://openalex.org/W4384663444","doi":"https://doi.org/10.1002/prot.26552","pmid":"https://pubmed.ncbi.nlm.nih.gov/37465978"},"language":"en","primary_location":{"id":"doi:10.1002/prot.26552","doi":"https://doi.org/10.1002/prot.26552","is_oa":true,"landing_page_url":"https://doi.org/10.1002/prot.26552","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.26552","source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.26552","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025256341","display_name":"Annika Topitsch","orcid":"https://orcid.org/0000-0002-3382-9670","observed_orcids":["https://orcid.org/0000-0002-3382-9670"]},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Annika Topitsch","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-3382-9670","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049569891","display_name":"Torsten F. Schwede","orcid":"https://orcid.org/0000-0003-2715-335X","observed_orcids":["https://orcid.org/0000-0003-2715-335X"]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Torsten Schwede","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2715-335X","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041584450","display_name":"Joana Pereira","orcid":"https://orcid.org/0000-0002-5588-6588","observed_orcids":["https://orcid.org/0000-0002-5588-6588"]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Joana Pereira","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5588-6588","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041584450","https://openalex.org/A5049569891"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I1850255"],"apc_list":{"value":4120,"currency":"USD","value_usd":4120},"apc_paid":{"value":4120,"currency":"USD","value_usd":4120},"fwci":0.6951,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62165876,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"92","issue":"1","first_page":"3","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9467999935150146,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9467999935150146,"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":0.03460000082850456,"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/T11162","display_name":"Enzyme Structure and Function","score":0.006500000134110451,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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-beta-barrel","display_name":"transmembrane beta-barrel","score":0.8730000257492065},{"id":"https://openalex.org/keywords/alphafold2","display_name":"AlphaFold2","score":0.871999979019165},{"id":"https://openalex.org/keywords/membrane-protein-structure-prediction","display_name":"membrane protein structure prediction","score":0.9240000247955322},{"id":"https://openalex.org/keywords/gram-negative-bacterial-outer-membrane","display_name":"Gram-negative bacterial outer membrane","score":0.7950000166893005},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"homology modeling","score":0.6830000281333923},{"id":"https://openalex.org/keywords/barros","display_name":"Barros","score":0.703000009059906}],"concepts":[{"id":"https://openalex.org/C172227984","wikidata":"https://www.wikidata.org/wiki/Q1400397","display_name":"Barrel (horology)","level":2,"score":0.7181506156921387},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.6668504476547241},{"id":"https://openalex.org/C146587185","wikidata":"https://www.wikidata.org/wiki/Q258248","display_name":"Bacterial outer membrane","level":4,"score":0.6377464532852173},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.6301449537277222},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5285419821739197},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.524832546710968},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.48179715871810913},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.4653549790382385},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.46007591485977173},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4443408250808716},{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.43707767128944397},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3984748125076294},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35948646068573},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.3593101501464844},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3442244827747345},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.336946964263916},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3222235441207886},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17223235964775085},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1559421718120575},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14777302742004395},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14694344997406006},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.11495736241340637},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.114373117685318},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","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}],"mesh":[{"descriptor_ui":"D001425","descriptor_name":"Bacterial Outer Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005668","descriptor_name":"Furylfuramide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1002/prot.26552","doi":"https://doi.org/10.1002/prot.26552","is_oa":true,"landing_page_url":"https://doi.org/10.1002/prot.26552","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.26552","source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2022.10.09.511469","doi":"https://doi.org/10.1101/2022.10.09.511469","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.10.09.511469","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/10/09/2022.10.09.511469.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:37465978","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37465978","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":"Proteins","raw_type":"Journal Article"},{"id":"pmh:oai:edoc.unibas.ch:90659","doi":null,"is_oa":false,"landing_page_url":"https://edoc.unibas.ch/90659/1/20221129085954_6385bbfa44734.pdf","pdf_url":"https://edoc.unibas.ch/90659/1/20221129085954_6385bbfa44734.pdf","source":{"id":"https://openalex.org/S4306401836","display_name":"edoc (University of Basel)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1850255","host_organization_name":"University of Basel","host_organization_lineage":["https://openalex.org/I1850255"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Preprint"},{"id":"pmh:oai:freidok.uni-freiburg.de:282063","doi":null,"is_oa":false,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:bsz:25-freidok-2820638","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proteins : structure, function, and bioinformatics. - 92, 1 (2024) , 3-14, ISSN: 1097-0134","raw_type":"article"},{"id":"pmh:oai:freidok.uni-freiburg.de:282064","doi":null,"is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/282064","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"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":"preprint"},{"id":"doi:10.5451/unibas-ep90659","doi":"https://doi.org/10.5451/unibas-ep90659","is_oa":true,"landing_page_url":"https://doi.org/10.5451/unibas-ep90659","pdf_url":null,"source":{"id":"https://openalex.org/S4306401836","display_name":"edoc (University of Basel)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1850255","host_organization_name":"University of Basel","host_organization_lineage":["https://openalex.org/I1850255"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1002/prot.26552","doi":"https://doi.org/10.1002/prot.26552","is_oa":true,"landing_page_url":"https://doi.org/10.1002/prot.26552","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.26552","source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310466","display_name":"Universit\u00e4t Basel","ror":"https://ror.org/02s6k3f65"},{"id":"https://openalex.org/F4320331322","display_name":"Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4384663444.pdf","grobid_xml":"https://content.openalex.org/works/W4384663444.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W1821139715","https://openalex.org/W1965540415","https://openalex.org/W1976179956","https://openalex.org/W1986541454","https://openalex.org/W1987438054","https://openalex.org/W2004691211","https://openalex.org/W2008708467","https://openalex.org/W2014101652","https://openalex.org/W2034453568","https://openalex.org/W2049357350","https://openalex.org/W2060388198","https://openalex.org/W2073895233","https://openalex.org/W2085212975","https://openalex.org/W2085368404","https://openalex.org/W2100511653","https://openalex.org/W2102245393","https://openalex.org/W2105899060","https://openalex.org/W2121547673","https://openalex.org/W2132022337","https://openalex.org/W2138217546","https://openalex.org/W2140673705","https://openalex.org/W2140831051","https://openalex.org/W2145268834","https://openalex.org/W2149525061","https://openalex.org/W2149605074","https://openalex.org/W2152811165","https://openalex.org/W2161193937","https://openalex.org/W2164056141","https://openalex.org/W2170231318","https://openalex.org/W2171007653","https://openalex.org/W2195753589","https://openalex.org/W2292314415","https://openalex.org/W2331160130","https://openalex.org/W2508425869","https://openalex.org/W2510407459","https://openalex.org/W2557215068","https://openalex.org/W2742457004","https://openalex.org/W2751260413","https://openalex.org/W2760320363","https://openalex.org/W2794345243","https://openalex.org/W2802099741","https://openalex.org/W2804822363","https://openalex.org/W2893650506","https://openalex.org/W2898210859","https://openalex.org/W2899749851","https://openalex.org/W2902746516","https://openalex.org/W2911430694","https://openalex.org/W2914884889","https://openalex.org/W2937530812","https://openalex.org/W2950795749","https://openalex.org/W2950954328","https://openalex.org/W2989453214","https://openalex.org/W3108574850","https://openalex.org/W3112376646","https://openalex.org/W3113163651","https://openalex.org/W3150245548","https://openalex.org/W3177828909","https://openalex.org/W3178087467","https://openalex.org/W3183420363","https://openalex.org/W3185358186","https://openalex.org/W3198923619","https://openalex.org/W3199246256","https://openalex.org/W3202105508","https://openalex.org/W3211795435","https://openalex.org/W4200140556","https://openalex.org/W4205172550","https://openalex.org/W4205296878","https://openalex.org/W4243601081","https://openalex.org/W4255594044","https://openalex.org/W4288428465","https://openalex.org/W4293475204","https://openalex.org/W4365137095","https://openalex.org/W6837419209"],"related_works":["https://openalex.org/W2137095432","https://openalex.org/W2121547673","https://openalex.org/W2171007653","https://openalex.org/W2169317607","https://openalex.org/W2042281452","https://openalex.org/W1821139715","https://openalex.org/W7100056117","https://openalex.org/W61784195","https://openalex.org/W2510407459","https://openalex.org/W7097124361"],"abstract_inverted_index":{"Most":[0],"proteins":[1],"found":[2],"in":[3,23,82,120,205],"the":[4,14,50,72,100,105,116,121,136,168,178,186,193,196],"outer":[5,18],"membrane":[6,19,89,151],"of":[7,33,42,49,102,118,123,128,138,167,170,199],"gram-negative":[8],"bacteria":[9],"share":[10],"a":[11,30,40,63],"common":[12],"domain:":[13],"transmembrane":[15,160,201],"\u03b2-barrel.":[16],"These":[17,181],"\u03b2-barrels":[20],"(OMBBs)":[21],"occur":[22],"multiple":[24],"sizes":[25],"and":[26,125,142,191],"different":[27],"families":[28],"with":[29,146],"wide":[31],"range":[32],"functions":[34],"evolved":[35],"independently":[36,166],"by":[37,59,189],"amplification":[38],"from":[39,177],"pool":[41],"homologous":[43],"ancestral":[44],"\u03b2\u03b2-hairpins.":[45],"This":[46],"is":[47,62],"part":[48],"reason":[51],"why":[52],"predicting":[53],"their":[54,97],"three-dimensional":[55],"(3D)":[56],"structure,":[57],"especially":[58,91],"homology":[60],"modeling,":[61],"major":[64],"challenge.":[65],"Recently,":[66],"DeepMind's":[67],"AlphaFold":[68],"v2":[69],"(AF2)":[70],"became":[71],"first":[73],"structure":[74],"prediction":[75,122],"method":[76],"to":[77,195],"reach":[78],"close-to-experimental":[79],"atomic":[80],"accuracy":[81,165],"CASP":[83],"even":[84,172],"for":[85,108,135,173],"difficult":[86],"targets.":[87],"However,":[88],"proteins,":[90],"OMBBs,":[92],"were":[93],"not":[94],"abundant":[95],"during":[96],"training,":[98],"raising":[99],"question":[101],"how":[103],"accurate":[104],"predictions":[106],"are":[107],"these":[109],"families.":[110],"In":[111,144],"this":[112],"study,":[113],"we":[114],"assessed":[115],"performance":[117],"AF2":[119,158,190],"OMBBs":[124],"OMBB-like":[126],"folds":[127],"various":[129],"topologies":[130,175,203],"using":[131],"an":[132],"in-house-developed":[133],"tool":[134],"analysis":[137],"OMBB":[139,207],"3D":[140],"structures,":[141],"barrOs.":[143],"agreement":[145],"previous":[147],"studies":[148,209],"on":[149,185],"other":[150],"protein":[152],"classes,":[153],"our":[154],"results":[155,182],"indicate":[156],"that":[157],"predicts":[159],"\u03b2-barrel":[161,202],"structures":[162],"at":[163],"high":[164],"use":[169],"templates,":[171],"novel":[174,200],"absent":[176],"training":[179],"set.":[180],"provide":[183],"confidence":[184],"models":[187],"generated":[188],"open":[192],"door":[194],"structural":[197],"elucidation":[198],"identified":[204],"high-throughput":[206],"annotation":[208],"or":[210],"designed":[211],"de":[212],"novo.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2023-07-20T00:00:00"}
