DAMPD: A manually curated antimicrobial peptide database

Handle URI:
http://hdl.handle.net/10754/325451
Title:
DAMPD: A manually curated antimicrobial peptide database
Authors:
Seshadri Sundararajan, Vijayaraghava; Gabere, Musa Nur; Pretorius, Ashley; Adam, Saleem; Christoffels, Alan; Lehväslaiho, Minna; Archer, John A.C. ( 0000-0002-3302-3933 ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
The demand for antimicrobial peptides (AMPs) is rising because of the increased occurrence of pathogens that are tolerant or resistant to conventional antibiotics. Since naturally occurring AMPs could serve as templates for the development of new anti-infectious agents to which pathogens are not resistant, a resource that contains relevant information on AMP is of great interest. To that extent, we developed the Dragon Antimicrobial Peptide Database (DAMPD, http://apps.sanbi.ac.za/dampd) that contains 1232 manually curated AMPs. DAMPD is an update and a replacement of the ANTIMIC database. In DAMPD an integrated interface allows in a simple fashion querying based on taxonomy, species, AMP family, citation, keywords and a combination of search terms and fields (Advanced Search). A number of tools such as Blast, ClustalW, HMMER, Hydrocalculator, SignalP, AMP predictor, as well as a number of other resources that provide additional information about the results are also provided and integrated into DAMPD to augment biological analysis of AMPs. The Author(s) 2011. Published by Oxford University Press.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Seshadri Sundararajan V, Gabere MN, Pretorius A, Adam S, Christoffels A, et al. (2012) DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Research 40: D1108-D1112. doi:10.1093/nar/gkr1063.
Publisher:
Oxford University Press
Journal:
Nucleic Acids Research
Issue Date:
21-Nov-2011
DOI:
10.1093/nar/gkr1063
PubMed ID:
22110032
PubMed Central ID:
PMC3244992
Type:
Article
ISSN:
03051048
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorSeshadri Sundararajan, Vijayaraghavaen
dc.contributor.authorGabere, Musa Nuren
dc.contributor.authorPretorius, Ashleyen
dc.contributor.authorAdam, Saleemen
dc.contributor.authorChristoffels, Alanen
dc.contributor.authorLehväslaiho, Minnaen
dc.contributor.authorArcher, John A.C.en
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2014-08-27T09:51:53Z-
dc.date.available2014-08-27T09:51:53Z-
dc.date.issued2011-11-21en
dc.identifier.citationSeshadri Sundararajan V, Gabere MN, Pretorius A, Adam S, Christoffels A, et al. (2012) DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Research 40: D1108-D1112. doi:10.1093/nar/gkr1063.en
dc.identifier.issn03051048en
dc.identifier.pmid22110032en
dc.identifier.doi10.1093/nar/gkr1063en
dc.identifier.urihttp://hdl.handle.net/10754/325451en
dc.description.abstractThe demand for antimicrobial peptides (AMPs) is rising because of the increased occurrence of pathogens that are tolerant or resistant to conventional antibiotics. Since naturally occurring AMPs could serve as templates for the development of new anti-infectious agents to which pathogens are not resistant, a resource that contains relevant information on AMP is of great interest. To that extent, we developed the Dragon Antimicrobial Peptide Database (DAMPD, http://apps.sanbi.ac.za/dampd) that contains 1232 manually curated AMPs. DAMPD is an update and a replacement of the ANTIMIC database. In DAMPD an integrated interface allows in a simple fashion querying based on taxonomy, species, AMP family, citation, keywords and a combination of search terms and fields (Advanced Search). A number of tools such as Blast, ClustalW, HMMER, Hydrocalculator, SignalP, AMP predictor, as well as a number of other resources that provide additional information about the results are also provided and integrated into DAMPD to augment biological analysis of AMPs. The Author(s) 2011. Published by Oxford University Press.en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0en
dc.subjectpolypeptide antibiotic agenten
dc.subjectautomationen
dc.subjectcataloging databaseen
dc.subjectcomparative studyen
dc.subjectcomputer interfaceen
dc.subjectcomputer programen
dc.subjectdata baseen
dc.subjectdragon antimicrobial peptide databaseen
dc.subjectdrug researchen
dc.subjectdrug screeningen
dc.subjectinformation retrievalen
dc.subjectonline systemen
dc.subjectprocess developmenten
dc.subjectAnti-Infective Agentsen
dc.subjectAntimicrobial Cationic Peptidesen
dc.subjectDatabases, Factualen
dc.subjectSoftwareen
dc.titleDAMPD: A manually curated antimicrobial peptide databaseen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNucleic Acids Researchen
dc.identifier.pmcidPMC3244992en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionSouth African National Bioinformatics Institute, University of the Western Cape, 7535 Bellville, South Africaen
dc.contributor.institutionSchool of Computer Engineering, Nanyang Technological University, 639 798 Singapore, Singaporeen
dc.contributor.institutionDepartment of Biotechnology, University of the Western Cape, 7535 Bellville, South Africaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorArcher, John A.C.en
kaust.authorBajic, Vladimir B.en
kaust.authorLehvas̈laiho, Minna H.en

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