APD3: The antimicrobial peptide database as a tool for research and education

Guangshun Wang, Xia Li, Zhe Wang

Research output: Contribution to journalArticle

387 Citations (Scopus)

Abstract

The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/) is an original database initially online in 2003. The APD2 (2009 version) has been regularly updated and further expanded into the APD3. This database currently focuses on natural antimicrobial peptides (AMPs) with defined sequence and activity. It includes a total of 2619 AMPs with 261 bacteriocins from bacteria, 4 AMPs from archaea, 7 from protists, 13 from fungi, 321 from plants and 1972 animal host defense peptides. The APD3 contains 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic and 185 anticancer peptides. Newly annotated are AMPswith antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties. We also describe other searchable annotations, including target pathogens, molecule-binding partners, post-translational modifications and animal models. Amino acid profiles or signatures of natural AMPs are important for peptide classification, prediction and design. Finally, we summarize various database applications in research and education.

Original languageEnglish (US)
Pages (from-to)D1087-D1093
JournalNucleic acids research
Volume44
Issue numberD1
DOIs
StatePublished - Jan 1 2016

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Databases
Education
Peptides
Research
pamidronate
Antiparasitic Agents
Bacteriocins
Archaea
Antimalarials
Post Translational Protein Processing
Wound Healing
Antiviral Agents
Peptide Hydrolases
Fungi
Animal Models
Antioxidants
HIV
Bacteria
Amino Acids

ASJC Scopus subject areas

  • Genetics

Cite this

APD3 : The antimicrobial peptide database as a tool for research and education. / Wang, Guangshun; Li, Xia; Wang, Zhe.

In: Nucleic acids research, Vol. 44, No. D1, 01.01.2016, p. D1087-D1093.

Research output: Contribution to journalArticle

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