{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T21:54:40Z","timestamp":1777499680940,"version":"3.51.4"},"reference-count":65,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2022,11,26]],"date-time":"2022-11-26T00:00:00Z","timestamp":1669420800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["CRC 1279"],"award-info":[{"award-number":["CRC 1279"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["EXC 2033"],"award-info":[{"award-number":["EXC 2033"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["CRC 1430"],"award-info":[{"award-number":["CRC 1430"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["Project-ID: 436586093"],"award-info":[{"award-number":["Project-ID: 436586093"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["UIDB\/04423\/2020 and UIDP\/04423\/2020"],"award-info":[{"award-number":["UIDB\/04423\/2020 and UIDP\/04423\/2020"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Portuguese Foundation for Science and Technology (Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014FCT)","award":["CRC 1279"],"award-info":[{"award-number":["CRC 1279"]}]},{"name":"Portuguese Foundation for Science and Technology (Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014FCT)","award":["EXC 2033"],"award-info":[{"award-number":["EXC 2033"]}]},{"name":"Portuguese Foundation for Science and Technology (Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014FCT)","award":["CRC 1430"],"award-info":[{"award-number":["CRC 1430"]}]},{"name":"Portuguese Foundation for Science and Technology (Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014FCT)","award":["Project-ID: 436586093"],"award-info":[{"award-number":["Project-ID: 436586093"]}]},{"name":"Portuguese Foundation for Science and Technology (Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014FCT)","award":["UIDB\/04423\/2020 and UIDP\/04423\/2020"],"award-info":[{"award-number":["UIDB\/04423\/2020 and UIDP\/04423\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Multi-drug resistance in bacteria is a major health problem worldwide. To overcome this issue, new approaches allowing for the identification and development of antibacterial agents are urgently needed. Peptides, due to their binding specificity and low expected side effects, are promising candidates for a new generation of antibiotics. For over two decades, a large diversity of antimicrobial peptides (AMPs) has been discovered and annotated in public databases. The AMP family encompasses nearly 20 biological functions, thus representing a potentially valuable resource for data mining analyses. Nonetheless, despite the availability of machine learning-based approaches focused on AMPs, these tools lack evidence of successful application for AMPs\u2019 discovery, and many are not designed to predict a specific function for putative AMPs, such as antibacterial activity. Consequently, among the apparent variety of data mining methods to screen peptide sequences for antibacterial activity, only few tools can deal with such task consistently, although with limited precision and generally no information about the possible targets. Here, we addressed this gap by introducing a tool specifically designed to identify antibacterial peptides (ABPs) with an estimation of which type of bacteria is susceptible to the action of these peptides, according to their response to the Gram-staining assay. Our tool is freely available via a web server named ABP-Finder. This new method ranks within the top state-of-the-art ABP predictors, particularly in terms of precision. Importantly, we showed the successful application of ABP-Finder for the screening of a large peptide library from the human urine peptidome and the identification of an antibacterial peptide.<\/jats:p>","DOI":"10.3390\/antibiotics11121708","type":"journal-article","created":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T03:28:49Z","timestamp":1669606129000},"page":"1708","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["ABP-Finder: A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria"],"prefix":"10.3390","volume":"11","author":[{"given":"Yasser B.","family":"Ruiz-Blanco","sequence":"first","affiliation":[{"name":"Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany"}]},{"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"}]},{"given":"Sandra","family":"Romero-Molina","sequence":"additional","affiliation":[{"name":"Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany"}]},{"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7793-4408","authenticated-orcid":false,"given":"Lia-Raluca","family":"Olari","sequence":"additional","affiliation":[{"name":"Institute of Molecular Virology, University Hospital Ulm, 89081 Ulm, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7552-8764","authenticated-orcid":false,"given":"Barbara","family":"Spellerberg","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7316-7141","authenticated-orcid":false,"given":"Jan","family":"M\u00fcnch","sequence":"additional","affiliation":[{"name":"Institute of Molecular Virology, University Hospital Ulm, 89081 Ulm, Germany"}]},{"given":"Elsa","family":"Sanchez-Garcia","sequence":"additional","affiliation":[{"name":"Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1007\/s12668-019-00658-4","article-title":"World Health Organization Report: Current Crisis of Antibiotic Resistance","volume":"9","author":"Rizvanov","year":"2019","journal-title":"BioNanoScience"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis","volume":"399","year":"2022","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1124\/pr.55.1.2","article-title":"Mechanisms of antimicrobial peptide action and resistance","volume":"55","author":"Yeaman","year":"2003","journal-title":"Pharmacol. 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