{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T15:09:22Z","timestamp":1778857762322,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination.<\/jats:p>\n               <jats:p>Availability: AMPA is freely available on the web at http:\/\/tcoffee.crg.cat\/apps\/ampa. The source code is also available in the web.<\/jats:p>\n               <jats:p>Contact: \u00a0marc.torrent@upf.edu; david.andreu@upf.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr604","type":"journal-article","created":{"date-parts":[[2011,11,4]],"date-time":"2011-11-04T01:43:06Z","timestamp":1320370986000},"page":"130-131","source":"Crossref","is-referenced-by-count":147,"title":["AMPA: an automated web server for prediction of protein antimicrobial regions"],"prefix":"10.1093","volume":"28","author":[{"given":"Marc","family":"Torrent","sequence":"first","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"},{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Di Tommaso","sequence":"additional","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Pulido","sequence":"additional","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. Vict\u00f2ria","family":"Nogu\u00e9s","sequence":"additional","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cedric","family":"Notredame","sequence":"additional","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ester","family":"Boix","sequence":"additional","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Andreu","sequence":"additional","affiliation":[{"name":"1 Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, 2Department of Biochemistry and Molecular Biology, Universitat Aut\u00f2noma de Barcelona, Biosciences Faculty, Cerdanyola del Vall\u00e8s and 3Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Dr Aiguader 88, 08003, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,11,3]]},"reference":[{"key":"2023061011444973600_B1","doi-asserted-by":"crossref","first-page":"2006","DOI":"10.1021\/jm8015365","article-title":"Identification of novel antibacterial peptides by chemoinformatics and machine learning","volume":"52","author":"Fjell","year":"2009","journal-title":"J. Med. Chem."},{"key":"2023061011444973600_B2","doi-asserted-by":"crossref","first-page":"1872","DOI":"10.2174\/156802610793176648","article-title":"Strategies for the discovery and advancement of novel cationic antimicrobial peptides","volume":"10","author":"Hadley","year":"2010","journal-title":"Curr. Top Med. Chem."},{"key":"2023061011444973600_B3","doi-asserted-by":"crossref","first-page":"157","DOI":"10.2174\/157019311795177781","article-title":"Identifying novel antimicrobial peptides with therapeutic potential against multidrug-resistant bacteria by using the SPOT synthesis","volume":"8","author":"Hilpert","year":"2011","journal-title":"Mini Rev. Org. Chem."},{"key":"2023061011444973600_B4","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1038\/nbt1113","article-title":"High-throughput generation of small antibacterial peptides with improved activity","volume":"23","author":"Hilpert","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023061011444973600_B5","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1186\/1471-2105-8-263","article-title":"Analysis and prediction of antibacterial peptides","volume":"8","author":"Lata","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023061011444973600_B6","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: a novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023061011444973600_B7","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/S1286-4579(02)01549-6","article-title":"Cathelicidins: microbicidal activity, mechanisms of action, and roles in innate immunity","volume":"4","author":"Ramanathan","year":"2002","journal-title":"Microbes Infect."},{"key":"2023061011444973600_B8","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1042\/BJ20082330","article-title":"Bactericidal and membrane disruption activities of the eosinophil cationic protein are largely retained in an N-terminal fragment","volume":"421","author":"Torrent","year":"2009","journal-title":"Biochem. J."},{"key":"2023061011444973600_B9","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/1471-2105-10-373","article-title":"A theoretical approach to spot active regions in antimicrobial proteins","volume":"10","author":"Torrent","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023061011444973600_B10","doi-asserted-by":"crossref","first-page":"e16968","DOI":"10.1371\/journal.pone.0016968","article-title":"Connecting peptide physicochemical and antimicrobial properties by a rational prediction model","volume":"6","author":"Torrent","year":"2011","journal-title":"PLoS One"},{"key":"2023061011444973600_B11","doi-asserted-by":"crossref","first-page":"e18476","DOI":"10.1371\/journal.pone.0018476","article-title":"Prediction of antimicrobial peptides based on sequence alignment and feature selection methods","volume":"6","author":"Wang","year":"2011","journal-title":"PLoS One"},{"key":"2023061011444973600_B12","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1021\/cb1001558","article-title":"Describing the mechanism of antimicrobial peptide action with the interfacial activity model","volume":"5","author":"Wimley","year":"2010","journal-title":"ACS Chem. Biol."},{"key":"2023061011444973600_B13","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1007\/s00018-011-0710-x","article-title":"Multifunctional cationic host defence peptides and their clinical applications","volume":"68","author":"Yeung","year":"2011","journal-title":"Cell Mol. Life Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/130\/50568301\/bioinformatics_28_1_130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/130\/50568301\/bioinformatics_28_1_130.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:46:12Z","timestamp":1686397572000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/1\/130\/219867"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,3]]},"references-count":13,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr604","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,1]]},"published":{"date-parts":[[2011,11,3]]}}}