{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T03:21:15Z","timestamp":1771644075720,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["UMO-2018\/31\/B\/NZ1\/04016"],"award-info":[{"award-number":["UMO-2018\/31\/B\/NZ1\/04016"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Biology Organization","award":["2057"],"award-info":[{"award-number":["2057"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1720342"],"award-info":[{"award-number":["1720342"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e.\u00a0minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https:\/\/alphaknot.cent.uw.edu.pl\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac388","type":"journal-article","created":{"date-parts":[[2022,5,7]],"date-time":"2022-05-07T03:34:01Z","timestamp":1651894441000},"page":"W44-W50","source":"Crossref","is-referenced-by-count":35,"title":["AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4167-1807","authenticated-orcid":false,"given":"Wanda","family":"Niemyska","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"},{"name":"Faculty of Mathematics, Informatics and Mechanics, University of Warsaw , Banacha 2,\u00a002-097 Warsaw, Poland"}]},{"given":"Pawel","family":"Rubach","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"},{"name":"Warsaw School of Economics, Al.\u00a0Niepodleglosci 162, 02-554, Warsaw, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9971-6807","authenticated-orcid":false,"given":"Bartosz A","family":"Gren","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"}]},{"given":"Mai\u00a0Lan","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"},{"name":"Polish-Japanese Academy of Information Technology , Koszykowa 86, 02-008 Warsaw, Poland"}]},{"given":"Wojciech","family":"Garstka","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"},{"name":"Inter-faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw ,\u00a0Banacha 2c, 02-097 Warsaw, Poland"}]},{"given":"Fernando","family":"Bruno\u00a0da\u00a0Silva","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"}]},{"given":"Eric\u00a0J","family":"Rawdon","sequence":"additional","affiliation":[{"name":"University of St.\u00a0Thomas , 2115 Summit Ave, Saint Paul, MN 55105, USA"}]},{"given":"Joanna\u00a0I","family":"Sulkowska","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Banacha 2c, Warsaw, Poland"}]}],"member":"286","published-online":{"date-parts":[[2022,5,24]]},"reference":[{"key":"2022070500003585400_B1","doi-asserted-by":"crossref","first-page":"D306","DOI":"10.1093\/nar\/gku1059","article-title":"KnotProt: a database of proteins with knots and slipknots","volume":"43","author":"Jamroz","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2022070500003585400_B2","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.sbi.2020.01.007","article-title":"On folding of entangled proteins: knots, lassos, links and \u03b8-curves","volume":"60","author":"Sulkowska","year":"2020","journal-title":"Curr. 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