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

Nucleic Acids Res. 2016 Jan 4;44(D1):D1087-93. doi: 10.1093/nar/gkv1278. Epub 2015 Nov 23.


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 AMPs with 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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acids / chemistry
  • Animals
  • Anti-Infective Agents / chemistry*
  • Anti-Infective Agents / pharmacology
  • Biomedical Research
  • Databases, Pharmaceutical*
  • Internet
  • Peptides / chemistry*
  • Peptides / pharmacology*


  • Amino Acids
  • Anti-Infective Agents
  • Peptides