{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T23:26:33Z","timestamp":1777591593623,"version":"3.51.4"},"reference-count":115,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T00:00:00Z","timestamp":1759449600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"USFQ MED","award":["2024-25"],"award-info":[{"award-number":["2024-25"]}]},{"name":"Portuguese Foundation for Science and Technology","award":["UIDB\/04423\/2020"],"award-info":[{"award-number":["UIDB\/04423\/2020"]}]},{"name":"Portuguese Foundation for Science and Technology","award":["UIDP\/04423\/2020"],"award-info":[{"award-number":["UIDP\/04423\/2020"]}]}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Computers"],"abstract":"<jats:p>Antiviral peptides (AVPs) are promising therapeutic candidates, yet the rapid growth of sequence data and the field\u2019s emphasis on predictors have left a gap: the lack of an integrated view linking peptide chemistry with biological context. Here, we map the AVP landscape through interactive data mining using Half-Space Proximal Networks (HSPNs) and Metadata Networks (MNs) in the StarPep toolbox. HSPNs minimize edges and avoid fixed thresholds, reducing computational cost while enabling high-resolution analysis. A threshold-free HSPN resolved eight chemically and biologically distinct communities, while MNs contextualized AVPs by source, function, and target, revealing structural\u2013functional relationships. To capture diversity compactly, we applied centrality-guided scaffold extraction with redundancy removal (90\u201350% identity), producing four representative subsets suitable for modeling and similarity searches. Alignment-free motif discovery yielded 33 validated motifs, including 10 overlapping with reported AVP signatures and 23 apparently novel. Motifs displayed category-specific enrichment across antimicrobial classes, and sequences carrying multiple motifs (\u22654\u20135) consistently showed higher predicted antiviral probabilities. Beyond computational insights, scaffolds provide representative \u201centry points\u201d into AVP chemical space, while motifs serve as modular building blocks for rational design. Together, these resources provide an integrated framework that may inform AVP discovery and support scaffold- and motif-guided therapeutic design.<\/jats:p>","DOI":"10.3390\/computers14100423","type":"journal-article","created":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T11:53:37Z","timestamp":1759492417000},"page":"423","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Mapping the Chemical Space of Antiviral Peptides with Half-Space Proximal and Metadata Networks Through Interactive Data Mining"],"prefix":"10.3390","volume":"14","author":[{"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"}]},{"given":"Yovani","family":"Marrero-Ponce","sequence":"additional","affiliation":[{"name":"Facultad de Ingenier\u00eda, Universidad Panamericana, Augusto Rodin No. 498, Insurgentes Mixcoac, Benito Ju\u00e1rez, Ciudad de M\u00e9xico 03920, Mexico"},{"name":"Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Universidad San Francisco de Quito (USFQ), Escuela de Medicina, Edificio de Especialidades M\u00e9dicas, Quito 170157, Pichincha, Ecuador"},{"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, s\/n, 4169-007 Porto, Portugal"}]},{"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"}]},{"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\/0000-0002-7503-1528","authenticated-orcid":false,"given":"Edgar A.","family":"M\u00e1rquez","sequence":"additional","affiliation":[{"name":"Grupo de Investigaciones en Qu\u00edmica y Biolog\u00eda, Departamento de Qu\u00edmica y Biolog\u00eda, Facultad de Ciencias B\u00e1sicas, Universidad del Norte, Carrera 51B, Km 5, V\u00eda Puerto Colombia, Barranquilla 081007, Colombia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6128-9504","authenticated-orcid":false,"given":"Jos\u00e9 R.","family":"Mora","sequence":"additional","affiliation":[{"name":"Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Universidad San Francisco de Quito (USFQ), Escuela de Medicina, Edificio de Especialidades M\u00e9dicas, Quito 170157, Pichincha, Ecuador"}]},{"given":"Felix","family":"Martinez-Rios","sequence":"additional","affiliation":[{"name":"Facultad de Ingenier\u00eda, Universidad Panamericana, Augusto Rodin No. 498, Insurgentes Mixcoac, Benito Ju\u00e1rez, Ciudad de M\u00e9xico 03920, Mexico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3710-0035","authenticated-orcid":false,"given":"Yunierkis","family":"P\u00e9rez-Castillo","sequence":"additional","affiliation":[{"name":"Bio-Cheminformatics Research Group and Escuela de Ciencias F\u00edsicas y Matem\u00e1ticas, Universidad de Las Am\u00e9ricas, Quito 170504, Pichincha, Ecuador"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Miranda, M.N.S., Pingarilho, M., Pimentel, V., Torneri, A., Seabra, S.G., Libin, P.J.K., and Abecasis, A.B. 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