{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T16:35:27Z","timestamp":1773246927097,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,11]],"date-time":"2019-01-11T00:00:00Z","timestamp":1547164800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["#2016\/21\/N\/NZ1\/02848"],"award-info":[{"award-number":["#2016\/21\/N\/NZ1\/02848"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Ministry of Science and Higher Education","award":["#0003\/ID3\/2016\/64"],"award-info":[{"award-number":["#0003\/ID3\/2016\/64"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink\u2014a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The PyLink plugin, manual and tutorial videos are available at http:\/\/pylink.cent.uw.edu.pl.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty1038","type":"journal-article","created":{"date-parts":[[2018,12,22]],"date-time":"2018-12-22T12:09:56Z","timestamp":1545480596000},"page":"3166-3168","source":"Crossref","is-referenced-by-count":13,"title":["PyLink: a PyMOL plugin to identify links"],"prefix":"10.1093","volume":"35","author":[{"given":"Aleksandra M","family":"Gierut","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Warsaw, Poland"},{"name":"Astronomy and Applied Computer Science, Jagiellonian University Faculty of Physics, , Cracow, Poland"}]},{"given":"Pawel","family":"Dabrowski-Tumanski","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Warsaw, Poland"},{"name":"University of Warsaw Faculty of Chemistry, , Warsaw, Poland"}]},{"given":"Wanda","family":"Niemyska","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Warsaw, Poland"}]},{"given":"Kenneth C","family":"Millett","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of California , Santa Barbara, CA, USA"}]},{"given":"Joanna I","family":"Sulkowska","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw , Warsaw, Poland"},{"name":"University of Warsaw Faculty of Chemistry, , Warsaw, Poland"}]}],"member":"286","published-online":{"date-parts":[[2019,1,11]]},"reference":[{"key":"2023062711310397700_bty1038-B1","doi-asserted-by":"crossref","first-page":"33872.","DOI":"10.1038\/srep33872","article-title":"Linking in domain-swapped protein dimers","volume":"6","author":"Baiesi","year":"2016","journal-title":"Sci. Rep"},{"key":"2023062711310397700_bty1038-B2","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.jmb.2011.10.018","article-title":"Oxidative folding and structural analyses of a kunitz-related inhibitor and its disulfide intermediates: functional implications","volume":"414","author":"Bronsoms","year":"2011","journal-title":"J. Mol. Biol"},{"key":"2023062711310397700_bty1038-B3","first-page":"251","article-title":"The cyclotides: novel macrocyclic peptides as scaffolds in drug design","volume":"5","author":"Craik","year":"2002","journal-title":"Curr. Opin. Drug Discov. Dev"},{"key":"2023062711310397700_bty1038-B4","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1006\/jmbi.1999.3383","article-title":"A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif craik, david j.; daly, norelle l.; bond, trudy; waine","volume":"294","author":"Cyclotides","year":"1999","journal-title":"J. Mol. Biol"},{"key":"2023062711310397700_bty1038-B5","doi-asserted-by":"crossref","first-page":"D243","DOI":"10.1093\/nar\/gkw976","article-title":"Linkprot: a database collecting information about biological links","volume":"45","author":"Dabrowski-Tumanski","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023062711310397700_bty1038-B6","doi-asserted-by":"crossref","first-page":"3415","DOI":"10.1073\/pnas.1615862114","article-title":"Topological knots and links in proteins","volume":"114","author":"Dabrowski-Tumanski","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062711310397700_bty1038-B7","doi-asserted-by":"crossref","first-page":"3819","DOI":"10.1093\/bioinformatics\/btx493","article-title":"Pylasso: a pymol plugin to identify lassos","volume":"33","author":"Gierut","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062711310397700_bty1038-B8","doi-asserted-by":"crossref","first-page":"11189","DOI":"10.1021\/ja00103a057","article-title":"Knots in proteins","volume":"116","author":"Liang","year":"1994","journal-title":"J. Am. Chem. Soc"},{"key":"2023062711310397700_bty1038-B9","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1093\/bioinformatics\/bts299","article-title":"Pyknot: a pymol tool for the discovery and analysis of knots in proteins","volume":"28","author":"Lua","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062711310397700_bty1038-B10","doi-asserted-by":"crossref","first-page":"e1000547.","DOI":"10.1371\/journal.pcbi.1000547","article-title":"Mechanical strength of 17 134 model proteins and cysteine slipknots","volume":"5","author":"Sikora","year":"2009","journal-title":"PLoS Comput. Biol"},{"key":"2023062711310397700_bty1038-B11","doi-asserted-by":"crossref","first-page":"225102.","DOI":"10.1063\/1.4985221","article-title":"Structural entanglements in protein complexes","volume":"146","author":"Zhao","year":"2017","journal-title":"J. Chem. Phys"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3166\/50719835\/bioinformatics_35_17_3166.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3166\/50719835\/bioinformatics_35_17_3166.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:31:57Z","timestamp":1687865517000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3166\/5288242"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,11]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty1038","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,11]]}}}