{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,14]],"date-time":"2025-12-14T08:26:33Z","timestamp":1765700793005,"version":"build-2065373602"},"reference-count":46,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T00:00:00Z","timestamp":1723593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"USFQ MED","award":["2023-4","UIDB\/04423\/913\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["2023-4","UIDB\/04423\/913\/2020","UIDP\/04423\/2020"]}]},{"name":"FCT","award":["2023-4","UIDB\/04423\/913\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["2023-4","UIDB\/04423\/913\/2020","UIDP\/04423\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Antiviral peptides (AVPs) represent a promising strategy for addressing the global challenges of viral infections and their growing resistances to traditional drugs. Lab-based AVP discovery methods are resource-intensive, highlighting the need for efficient computational alternatives. In this study, we developed five non-trained but supervised multi-query similarity search models (MQSSMs) integrated into the StarPep toolbox. Rigorous testing and validation across diverse AVP datasets confirmed the models\u2019 robustness and reliability. The top-performing model, M13+, demonstrated impressive results, with an accuracy of 0.969 and a Matthew\u2019s correlation coefficient of 0.71. To assess their competitiveness, the top five models were benchmarked against 14 publicly available machine-learning and deep-learning AVP predictors. The MQSSMs outperformed these predictors, highlighting their efficiency in terms of resource demand and public accessibility. Another significant achievement of this study is the creation of the most comprehensive dataset of antiviral sequences to date. In general, these results suggest that MQSSMs are promissory tools to develop good alignment-based models that can be successfully applied in the screening of large datasets for new AVP discovery.<\/jats:p>","DOI":"10.3390\/antibiotics13080768","type":"journal-article","created":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T06:23:05Z","timestamp":1723616585000},"page":"768","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Innovative Alignment-Based Method for Antiviral Peptide Prediction"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6910-7581","authenticated-orcid":false,"given":"Daniela","family":"de Llano Garc\u00eda","sequence":"first","affiliation":[{"name":"School of Chemical Sciences and Engineering, Yachay Tech University, Hda. San Jos\u00e9 s\/n y Proyecto Yachay, Urcuqu\u00ed 100119, Imbabura, Ecuador"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2721-1142","authenticated-orcid":false,"given":"Yovani","family":"Marrero-Ponce","sequence":"additional","affiliation":[{"name":"Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades M\u00e9dicas, Instituto de Simulaci\u00f3n Computacional (ISC-USFQ), Diego de Robles y v\u00eda Interoce\u00e1nica, Quito 170157, Pichincha, Ecuador"},{"name":"Facultad de Ingenier\u00eda, Universidad Panamericana, Augusto Rodin 498, Benito Ju\u00e1rez 03920, Ciudad de M\u00e9xico, Mexico"},{"name":"Computer Science Department, Universitat de Val\u00e8ncia, 46100 Valencia, Burjassot, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9908-2418","authenticated-orcid":false,"given":"Guillermin","family":"Ag\u00fcero-Chapin","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1543-3568","authenticated-orcid":false,"given":"Francesc J.","family":"Ferri","sequence":"additional","affiliation":[{"name":"Computer Science Department, Universitat de Val\u00e8ncia, 46100 Valencia, Burjassot, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal"}]},{"given":"Felix","family":"Martinez-Rios","sequence":"additional","affiliation":[{"name":"Facultad de Ingenier\u00eda, Universidad Panamericana, Augusto Rodin 498, Benito Ju\u00e1rez 03920, Ciudad de M\u00e9xico, Mexico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6910-5685","authenticated-orcid":false,"given":"Hortensia","family":"Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"School of Chemical Sciences and Engineering, Yachay Tech University, Hda. San Jos\u00e9 s\/n y Proyecto Yachay, Urcuqu\u00ed 100119, Imbabura, Ecuador"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5296","DOI":"10.1128\/JVI.00151-09","article-title":"Virology in the 21st Century","volume":"83","author":"Enquist","year":"2009","journal-title":"J. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1038\/s41392-022-00904-4","article-title":"Therapeutic Peptides: Current Applications and Future Directions","volume":"7","author":"Wang","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"4433","DOI":"10.1007\/s00018-016-2299-6","article-title":"Mechanisms of Viral Mutation","volume":"73","year":"2016","journal-title":"Cell. Mol. 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