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

TLDR

The antimicrobial peptide database (APD) began online in 2003, has evolved through APD2 to the current APD3, and highlights the importance of amino acid profiles for classifying, predicting, and designing natural AMPs. The study summarizes how the APD3 can be applied in research and education. APD3 catalogs natural AMPs with defined sequences and activities, annotating diverse functional properties such as antibiofilm, antimalarial, and wound healing, and provides searchable fields for target pathogens, binding partners, post‑translational modifications, and animal models. APD3 contains 2,619 AMPs, including 261 bacteriocins, 4 archaeal, 7 protist, 13 fungal, 321 plant, and 1,972 animal peptides, with 2,169 antibacterial, 172 antiviral, 105 anti‑HIV, 959 antifungal, 80 antiparasitic, and 185 anticancer entries.

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 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.