{"id":"https://openalex.org/W4282920722","doi":"https://doi.org/10.1093/nar/gkac388","title":"AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods","display_name":"AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods","publication_year":2022,"publication_date":"2022-05-07","ids":{"openalex":"https://openalex.org/W4282920722","doi":"https://doi.org/10.1093/nar/gkac388","pmid":"https://pubmed.ncbi.nlm.nih.gov/35609987"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac388","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W44/44379434/gkac388.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/50/W1/W44/44379434/gkac388.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058049197","display_name":"Wanda Niemyska","orcid":"https://orcid.org/0000-0003-4167-1807"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Wanda Niemyska","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","Faculty of Mathematics, Informatics and Mechanics, University of Warsaw , Banacha 2,\u00a002-097 Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0003-4167-1807","affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Faculty of Mathematics, Informatics and Mechanics, University of Warsaw , Banacha 2,\u00a002-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070820751","display_name":"Pawe\u0142 Rubach","orcid":"https://orcid.org/0000-0001-5487-609X"},"institutions":[{"id":"https://openalex.org/I18193975","display_name":"SGH Warsaw School of Economics","ror":"https://ror.org/032cph770","country_code":"PL","type":"education","lineage":["https://openalex.org/I18193975"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Pawel Rubach","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","Warsaw School of Economics, Al.\u00a0Niepodleglosci 162, 02-554, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Warsaw School of Economics, Al.\u00a0Niepodleglosci 162, 02-554, Warsaw, Poland","institution_ids":["https://openalex.org/I18193975"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062173177","display_name":"Bartosz A. Gren","orcid":"https://orcid.org/0000-0001-9971-6807"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Bartosz A Gren","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0001-9971-6807","affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082661201","display_name":"Mai Lan Nguyen","orcid":"https://orcid.org/0000-0001-8117-0391"},"institutions":[{"id":"https://openalex.org/I3017851245","display_name":"Polish-Japanese Academy of Information Technology","ror":"https://ror.org/01v542j61","country_code":"PL","type":"education","lineage":["https://openalex.org/I3017851245"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mai\u00a0Lan Nguyen","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","Polish-Japanese Academy of Information Technology , Koszykowa 86, 02-008 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Polish-Japanese Academy of Information Technology , Koszykowa 86, 02-008 Warsaw, Poland","institution_ids":["https://openalex.org/I3017851245"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062457980","display_name":"Wojciech Garstka","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Wojciech Garstka","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","Inter-faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw ,\u00a0Banacha 2c, 02-097 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Inter-faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw ,\u00a0Banacha 2c, 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068104605","display_name":"Fernando Bruno da Silva","orcid":"https://orcid.org/0000-0002-0285-8700"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Fernando Bruno\u00a0da\u00a0Silva","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075733920","display_name":"Eric J. Rawdon","orcid":"https://orcid.org/0000-0002-7190-8193"},"institutions":[{"id":"https://openalex.org/I161515732","display_name":"University of St. Thomas - Minnesota","ror":"https://ror.org/05vfxvp80","country_code":"US","type":"education","lineage":["https://openalex.org/I161515732"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric\u00a0J Rawdon","raw_affiliation_strings":["University of St.\u00a0Thomas , 2115 Summit Ave, Saint Paul, MN 55105, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of St.\u00a0Thomas , 2115 Summit Ave, Saint Paul, MN 55105, USA","institution_ids":["https://openalex.org/I161515732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013867366","display_name":"Joanna I. Su\u0142kowska","orcid":"https://orcid.org/0000-0003-2452-0724"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Joanna\u00a0I Sulkowska","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5013867366"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.0319,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.92585033,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"50","issue":"W1","first_page":"W44","last_page":"W50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/knot","display_name":"Knot (papermaking)","score":0.776275634765625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.712770938873291},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6196735501289368},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6188638806343079},{"id":"https://openalex.org/keywords/quantum-entanglement","display_name":"Quantum entanglement","score":0.46593087911605835},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42624929547309875},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4222133457660675},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.4187707304954529},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3744736611843109},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33770185708999634},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16910871863365173},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.16793745756149292},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16348570585250854},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09093940258026123}],"concepts":[{"id":"https://openalex.org/C2779863119","wikidata":"https://www.wikidata.org/wiki/Q6423048","display_name":"Knot (papermaking)","level":2,"score":0.776275634765625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.712770938873291},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6196735501289368},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6188638806343079},{"id":"https://openalex.org/C121040770","wikidata":"https://www.wikidata.org/wiki/Q215675","display_name":"Quantum entanglement","level":3,"score":0.46593087911605835},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42624929547309875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4222133457660675},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.4187707304954529},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3744736611843109},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33770185708999634},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16910871863365173},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.16793745756149292},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16348570585250854},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09093940258026123},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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/C42360764","wikidata":"https://www.wikidata.org/wiki/Q83588","display_name":"Chemical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","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":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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkac388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac388","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W44/44379434/gkac388.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:35609987","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35609987","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:ir.stthomas.edu:cas_mathpub-1201","is_oa":false,"landing_page_url":"https://ir.stthomas.edu/cas_mathpub/202","pdf_url":null,"source":{"id":"https://openalex.org/S4377196573","display_name":"UST Research Online (University of St. Thomas - Minnesota)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161515732","host_organization_name":"University of St. Thomas - Minnesota","host_organization_lineage":["https://openalex.org/I161515732"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Mathematics Faculty Publications &amp; Data","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:9252816","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9252816","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,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkac388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac388","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W44/44379434/gkac388.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G696086291","display_name":null,"funder_award_id":"1720342","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G800112019","display_name":null,"funder_award_id":"UMO-2018/31/B/NZ1/04016","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320323873","display_name":"Uniwersytet Warszawski","ror":"https://ror.org/039bjqg32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4282920722.pdf","grobid_xml":"https://content.openalex.org/works/W4282920722.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1985768873","https://openalex.org/W2019218232","https://openalex.org/W2050679015","https://openalex.org/W2155075558","https://openalex.org/W2807115333","https://openalex.org/W2899044544","https://openalex.org/W2901992705","https://openalex.org/W3005909868","https://openalex.org/W3087730481","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W4206596435"],"related_works":["https://openalex.org/W2626999804","https://openalex.org/W4250004941","https://openalex.org/W2736202444","https://openalex.org/W2049015391","https://openalex.org/W2137014442","https://openalex.org/W1533158771","https://openalex.org/W122082928","https://openalex.org/W2104288289","https://openalex.org/W2521397622","https://openalex.org/W4294067941"],"abstract_inverted_index":{"AlphaKnot":[0,16,175],"is":[1,60,71],"a":[2,25,38,63,77,119,163],"server":[3,149,176],"that":[4,117],"measures":[5],"entanglement":[6],"in":[7,30,42,62,73],"AlphaFold-solved":[8],"protein":[9,115,127,157,167],"models":[10,51],"while":[11],"considering":[12],"pLDDT":[13,133],"confidence":[14,134],"values.":[15],"has":[17],"two":[18],"main":[19],"functions:":[20],"(i)":[21],"providing":[22,37],"researchers":[23],"with":[24],"webserver":[26],"for":[27,49,86,92,125,153,166,170],"analyzing":[28],"knotting":[29,41,59,67],"their":[31],"own":[32],"AlphaFold":[33,43],"predictions":[34,44],"and":[35,91,142,159,169],"(ii)":[36],"database":[39,145],"of":[40,69,76,94,107,114,147],"from":[45],"the":[46,74,83,87,104,108,132,148],"21":[47],"proteomes":[48],"which":[50,80],"have":[52],"been":[53],"published":[54],"prior":[55],"to":[56,155],"2022.":[57],"The":[58,66,97,144,174],"defined":[61],"probabilistic":[64],"fashion.":[65],"complexity":[68],"proteins":[70],"presented":[72],"form":[75,118],"matrix":[78],"diagram":[79],"shows":[81],"users":[82],"knot":[84,99,109,121],"type":[85],"entire":[88],"polypeptide":[89],"chain":[90],"each":[93,126],"its":[95],"subchains.":[96],"dominant":[98],"types":[100],"as":[101,103,139,162],"well":[102],"computed":[105],"locations":[106],"cores":[110],"(i.e.":[111],"minimal":[112],"portions":[113],"backbones":[116],"given":[120],"type)":[122],"are":[123,137],"shown":[124],"structure.":[128],"Based":[129],"mainly":[130],"on":[131],"values,":[135],"entanglements":[136],"classified":[138],"Knots,":[140],"Unsure,":[141],"Artifacts.":[143],"portion":[146],"can":[150,177],"be":[151,178],"used,":[152],"example,":[154],"examine":[156],"geometry":[158],"entanglement-function":[160],"correlations,":[161],"reference":[164],"set":[165],"modeling,":[168],"facilitating":[171],"evolutional":[172],"studies.":[173],"found":[179],"at":[180],"https://alphaknot.cent.uw.edu.pl/.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}
