Unifying the classification of antimicrobial peptides in the antimicrobial peptide database

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Scopus citations


Natural products offer an important avenue to novel therapeutics against drug-resistant bacteria, viruses, fungi, parasites, and cancer. However, there are numerous hurdles and challenges in discovering such molecules, including antimicrobial peptides (AMPs). While a thorough characterization of AMPs is limited by the amount of material, existing technology, and researcher's expertise, peptide classification is complicated by incomplete information as well as different methods proposed for AMPs from bacteria, plants, and animals. This article describes unified classification schemes for natural AMPs on a common platform: the Antimicrobial Peptide Database (APD; https://aps.unmc.edu). The various criteria for these unified classifications include peptide biological source, biosynthesis machinery, biological activity, amino acid sequence, mechanism of action, and three-dimensional structure. To overcome the problem with a limited number of known 3D structures, a universal peptide classification has also been refined and executed in the APD database. This universal method, based on the spatial connection patterns of polypeptide chains, is independent of peptide source, size, activity, 3D structure, or mechanism of action. It facilitates information registration, naming, exchange, decoding, prediction, and design of novel antimicrobial peptides.

Original languageEnglish (US)
Title of host publicationAntimicrobial Peptides
EditorsLeslie M. Hicks
PublisherAcademic Press Inc.
Number of pages18
ISBN (Print)9780323901581
StatePublished - Jan 2022

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988


  • Antibiotics
  • Antimicrobial peptides
  • Classification
  • Database
  • Hydrophobic content
  • Net charge
  • Peptide discovery
  • Peptide length
  • Structure

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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