{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T18:16:04Z","timestamp":1772907364416,"version":"3.50.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T00:00:00Z","timestamp":1743033600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009558","name":"University Natural Science Research Project of Anhui Province","doi-asserted-by":"publisher","award":["2023AH050998"],"award-info":[{"award-number":["2023AH050998"]}],"id":[{"id":"10.13039\/501100009558","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Antiviral peptides (AVPs) are short chains of amino acids, showing great potential as antiviral drugs. The traditional wisdom (e.g. wet experiments) for identifying the AVPs is time-consuming and laborious, while cutting-edge computational methods are less accurate to predict them.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we propose an AVPs prediction model via biological words representation, dubbed AVPpred-BWR. Based on the fact that the secondary structures of AVPs mainly consist of \u03b1-helix and loop, we explore the biological words of 1mer (corresponding to loops) and 4mer (4 continuous residues, corresponding to \u03b1-helix). That is, the peptides sequences are decomposed into biological words, and then the concealed sequential information is represented by training the Word2Vec models. Moreover, in order to extract multi-scale features, we leverage a CNN-Transformer framework to process the embeddings of 1mer and 4mer generated by Word2Vec models. To the best of our knowledge, this is the first time to realize the word segmentation of protein primary structure sequences based on the regularity of protein secondary structure. AVPpred-BWR illustrates clear improvements over its competitors on the independent test set (e.g. improvements of 4.6% and 11.0% for AUROC and MCC, respectively, compared to UniDL4BioPep).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>AVPpred-BWR is publicly available at: https:\/\/github.com\/zyweizm\/AVPpred-BWR or https:\/\/zenodo.org\/records\/14880447 (doi: 10.5281\/zenodo.14880447).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf126","type":"journal-article","created":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T19:40:04Z","timestamp":1743277204000},"source":"Crossref","is-referenced-by-count":6,"title":["AVPpred-BWR: antiviral peptides prediction via biological words representation"],"prefix":"10.1093","volume":"41","author":[{"given":"Zhuoyu","family":"Wei","sequence":"first","affiliation":[{"name":"School of Information and Artificial Intelligence, Anhui Agricultural University , Hefei, Anhui 230036,","place":["China"]}]},{"given":"Yongqi","family":"Shen","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence, Anhui Agricultural University , Hefei, Anhui 230036,","place":["China"]}]},{"given":"Xiang","family":"Tang","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence, Anhui Agricultural University , Hefei, Anhui 230036,","place":["China"]}]},{"given":"Jian","family":"Wen","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence, Anhui Agricultural University , Hefei, Anhui 230036,","place":["China"]}]},{"given":"Youyi","family":"Song","sequence":"additional","affiliation":[{"name":"School of Science, China Pharmaceutical University , Nanjing 210009,","place":["China"]}]},{"given":"Mingqiang","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics , Nanjing 210016,","place":["China"]}]},{"given":"Jing","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence, Anhui Agricultural University , Hefei, Anhui 230036,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1967-2806","authenticated-orcid":false,"given":"Xiaolei","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Information and Artificial Intelligence, Anhui Agricultural University , Hefei, Anhui 230036,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,27]]},"reference":[{"key":"2025041602170947600_btaf126-B1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/s10989-020-10072-0","article-title":"Antiviral peptides: identification and validation","volume":"27","author":"Agarwal","year":"2021","journal-title":"Int J Peptide Res 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