{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T00:11:18Z","timestamp":1783815078538,"version":"3.55.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T00:00:00Z","timestamp":1680739200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100007907","name":"Kansas Agricultural Experimental Station","doi-asserted-by":"crossref","award":["23-192-J"],"award-info":[{"award-number":["23-192-J"]}],"id":[{"id":"10.13039\/100007907","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Agriculture and Food Research Initiative Competitive","award":["2020-68008-31408"],"award-info":[{"award-number":["2020-68008-31408"]}]},{"name":"Agriculture and Food Research Initiative Competitive","award":["2021-67021-34495"],"award-info":[{"award-number":["2021-67021-34495"]}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Global Food Systems initiative of Kansas State University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Identification of potent peptides through model prediction can reduce benchwork in wet experiments. However, the conventional process of model buildings can be complex and time consuming due to challenges such as peptide representation, feature selection, model selection and hyperparameter tuning. Recently, advanced pretrained deep learning-based language models (LMs) have been released for protein sequence embedding and applied to structure and function prediction. Based on these developments, we have developed UniDL4BioPep, a universal deep-learning model architecture for transfer learning in bioactive peptide binary classification modeling. It can directly assist users in training a high-performance deep-learning model with a fixed architecture and achieve cutting-edge performance to meet the demands in efficiently novel bioactive peptide discovery. To the best of our best knowledge, this is the first time that a pretrained biological language model is utilized for peptide embeddings and successfully predicts peptide bioactivities through large-scale evaluations of those peptide embeddings. The model was also validated through uniform manifold approximation and projection analysis. By combining the LM with a convolutional neural network, UniDL4BioPep achieved greater performances than the respective state-of-the-art models for 15 out of 20 different bioactivity dataset prediction tasks. The accuracy, Mathews correlation coefficient and area under the curve were 0.7\u20137, 1.23\u201326.7 and 0.3\u201325.6% higher, respectively. A user-friendly web server of UniDL4BioPep for the tested bioactivities is established and freely accessible at https:\/\/nepc2pvmzy.us-east-1.awsapprunner.com. The source codes, datasets and templates of UniDL4BioPep for other bioactivity fitting and prediction tasks are available at https:\/\/github.com\/dzjxzyd\/UniDL4BioPep.<\/jats:p>","DOI":"10.1093\/bib\/bbad135","type":"journal-article","created":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T04:30:30Z","timestamp":1680755430000},"source":"Crossref","is-referenced-by-count":127,"title":["UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity"],"prefix":"10.1093","volume":"24","author":[{"given":"Zhenjiao","family":"Du","sequence":"first","affiliation":[{"name":"Department of Grain Science and Industry, Kansas State University , Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingjian","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Kansas State University , Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixiang","family":"Xu","sequence":"additional","affiliation":[{"name":"Healthy Processed Foods Research Unit, Western Regional Research Center USDA-ARS , 800 Buchanan Street, Albany, CA 94710, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonghui","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Grain Science and Industry, Kansas State University , Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,5]]},"reference":[{"key":"2024040500022294800_ref1","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.tifs.2020.12.002","article-title":"Novel technologies for the production of bioactive peptides","volume":"108","author":"Ulug","year":"2021","journal-title":"Trends Food Sci Technol"},{"key":"2024040500022294800_ref2","first-page":"100353","article-title":"Review and 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