{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T05:19:28Z","timestamp":1788326368658,"version":"build-2803163510"},"reference-count":35,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T00:00:00Z","timestamp":1788048000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2022A1515011720"],"award-info":[{"award-number":["2022A1515011720"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Shantou Municipal Science and Technology Bureau","award":["STKJ2024065"],"award-info":[{"award-number":["STKJ2024065"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32570197"],"award-info":[{"award-number":["32570197"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"award":["32570197"],"award-info":[{"award-number":["32570197"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Accurate computational prediction of antiviral peptides (AVPs) can accelerate peptide screening and reduce experimental costs. However, existing deep learning-based methods still suffer from severe class imbalance, over-reliance on handcrafted features and limited interpretability. Here, we propose PMAVP, a multi-task learning framework that integrates the ProtT5 pre-trained protein language model with a Mamba-inspired module for AVP identification and functional activity prediction. We use ProtT5 to extract deep semantic representations from peptide sequences and a Mamba module to capture long-range dependencies at a lower computational complexity. We introduce Focal Loss to mitigate class imbalance and leverage transfer learning to enhance performance on functional activity prediction. Experimental results demonstrate that our model achieves superior performance in terms of prediction accuracy, stability, and computational efficiency. Furthermore, DeepSHAP-based interpretability analysis reveals that the first 40 amino acid residues contribute substantially to AVP prediction.<\/jats:p>","DOI":"10.3390\/ijms27177764","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T09:48:36Z","timestamp":1788256116000},"page":"7764","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["PMAVP: A Mamba-Inspired Deep Learning Framework for Antiviral Peptide Identification and Functional Activity Prediction"],"prefix":"10.3390","volume":"27","author":[{"given":"Peiwei","family":"Wei","sequence":"first","affiliation":[{"name":"Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou 515041, China"},{"name":"Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou 515041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weihao","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, College of Engineering, Shantou University, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6315-5809","authenticated-orcid":false,"given":"Qingsong","family":"Qin","sequence":"additional","affiliation":[{"name":"Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou 515041, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuliang","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, College of Engineering, Shantou University, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3575-4948","authenticated-orcid":false,"given":"Yi","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, College of Engineering, Shantou University, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4020-5687","authenticated-orcid":false,"given":"Guishan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, College of Engineering, Shantou University, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nature02759","article-title":"The challenge of emerging and re-emerging infectious diseases","volume":"430","author":"Morens","year":"2004","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Bloom, D.E., and Cadarette, D. 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