{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T15:43:31Z","timestamp":1775663011357,"version":"3.50.1"},"reference-count":25,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T00:00:00Z","timestamp":1771459200000},"content-version":"vor","delay-in-days":18,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","award":["291PEP"],"award-info":[{"award-number":["291PEP"]}],"id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2026,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    With antimicrobial resistance emerging as a top global health concern, new approaches to prevent and treat infections are urgently needed. Antimicrobial peptides are recognized as a promising alternative to conventional antibiotics. Considering the costly, labor\u2010intensive, and time\u2010consuming nature of wet lab screening, in recent years, proteomics research has increasingly relied on\n                    <jats:italic>in silico<\/jats:italic>\n                    methods to predict physicochemical, structural, and biological properties of candidate peptides. Here, we present the AMPSeek protocol to enable scientists to screen peptides and predict their potential antimicrobial activity, toxicity, and associated three\u2010dimensional structure with a single command. The AMPSeek framework integrates AMPlify, tAMPer, and LocalColabFold, scales efficiently with increasing sample size, and produces an interactive HyperText Markup Language report to facilitate result interpretation. We provide step\u2010by\u2010step instructions for installing and running AMPSeek on a ten\u2010peptide test set, along with two additional datasets (\n                    <jats:italic>n<\/jats:italic>\n                    \u00a0=\u00a020 and\n                    <jats:italic>n<\/jats:italic>\n                    = 100; mean peptide length \u2248121.3) to demonstrate AMPSeek's near\u2010linear scalability. AMPSeek is available on GitHub under the GPLv3 software license agreement:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/bcgsc\/AMPSeek\">https:\/\/github.com\/bcgsc\/AMPSeek<\/jats:ext-link>\n                    . \u00a9 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol<\/jats:bold>\n                    : Prediction of antimicrobial peptide activity, three\u2010dimensional structure, and toxicity\n                  <\/jats:p>","DOI":"10.1002\/cpz1.70325","type":"journal-article","created":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T15:08:34Z","timestamp":1771513714000},"source":"Crossref","is-referenced-by-count":0,"title":["AMPSeek: A Workflow for Predicting Antimicrobial Peptide Activity, Three\u2010Dimensional Structure, and Toxicity"],"prefix":"10.1002","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-7609-8971","authenticated-orcid":false,"given":"Emily","family":"Zhang","sequence":"first","affiliation":[{"name":"BC Cancer Vancouver BC Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Berke","family":"Ucar","sequence":"additional","affiliation":[{"name":"BC Cancer Vancouver BC Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali","family":"Salehi","sequence":"additional","affiliation":[{"name":"BC Cancer Vancouver BC Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ren\u00e9 L.","family":"Warren","sequence":"additional","affiliation":[{"name":"BC Cancer Vancouver BC Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[{"name":"BC Cancer Vancouver BC Canada"},{"name":"Department of Medical Genetics University of British Columbia  Columbia BC Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2026,2,19]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20290"},{"key":"e_1_2_6_3_1","doi-asserted-by":"crossref","unstructured":"Cho K. vanMerrienboer B. 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Schwenk H. &Bengio Y.(2014).Learning phrase representations using RNN Encoder\u2010Decoder for statistical machine translation [Preprint; version 3].arXiv 1406.1078.https:\/\/doi.org\/10.48550\/arxiv.1406.1078","DOI":"10.3115\/v1\/D14-1179"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3820"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.2174\/138161209788682325"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5076"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nnano.2010.29"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1267"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0177459"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010022\u201008310\u20104"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13104\u2010023\u201006279\u20101"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.5555\/2600239.2600241"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010022\u201001488\u20101"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140\u20106736(21)02724\u20100"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms12095971"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2004.09.005"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004445"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1109\/tnn.2008.2005605"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1109\/78.650093"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bsheal.2022.02.003"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmr.2019.07.013"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1596\/26707"},{"key":"e_1_2_6_23_1","unstructured":"World Health Organization. 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