Classification of Antimicrobial Peptides
This page lists the systematic classification methods for antimicrobial peptides. This was first initiated during 2009 and 2010 when Dr. Wang was editing the book Antimicrobial Peptides. For updated classification schemes, please refer to our recent publications at bottom.

1. Based on the biosynthetic machines

Natural peptides can be classified as ribosommaly synthesized peptides and non-ribosomal peptides made by multiple enzyme systems. This database focuses primarily on gene-coded peptides, which in some AMP scientists mind, are true AMPs. It is important to note that some non-ribosome synthesized peptide antibiotics in this database (e.g. gramicidins, colistin and daptomycin) are already in clinical use.

2. Based on biological sources

In the APD3, the natural sources of antimicrobial peptides cover six life kingdoms: bacteria, archaea, protists, fungi, plants, and animals. So, you can search bacterial AMPs (bacteriocins), plant AMPs, and animal AMPs. Animal AMPs are further classified into insect AMPs, amphibian AMPs, fish AMPs, reptile AMPs, mammal AMPs, etc based on source family names. The major and well-studied AMPs families in the animal kingdom are cathelicidins, defensins, and histatins. Bacteriocins are further classified (see Glossary).

3. Based on biological functions

wound healing,
ion channel inhibitor,

For a complete list, please refer to the main page of this database or go to the database search interface.

4. Based on peptide properties

In the absence of three-dimensional (3D) structural information, AMPs can be classified based on peptide properties such as charge, hydrophobicity, amino acid composition, and length.

Based on aa composition, there are amino acid-rich peptides (defined at least 25% in the APD). Examples are Trp-rich, His-rich, Pro-rich, Arg-rich, Gly-rich (classic), Leu-rich, Ser-rich, Lys-rich, Asp-rich, and Ala-rich AMPs (less popular). Based on our definition, we did not find AMPs rich in methinine, asparagine, and glutamine in the APD (2022) although they exist in proteins. For additional info, you can refer to our recent article.

Based on net charge, there are cationic (net charge > 0; 88%), neutral (net charge = 0; 6%), and anionic peptides (net charge <0; 6%).

Based on hydrophobic/hydrophilic amino acid composition, there are hydrophobic, amphipathic, and hydrophilic peptides based on hydrophobicity.

Also, natural AMPs can be arbitrarily classified based on peptide size (number of amino acids, aa): ultra-short (2-10 aa), short (10-24 aa), medium (25-50 aa), and long (50-100 aa). AMPs greater than 100 aa are antimicrobial proteins (e.g., lysozyme, histones, and RNase 7).

5. Based on covalent bonding patterns

This universal classification system (UC) categorizes antimicrobial peptides (or peptides in genenal) into four classes (Wang, G, 2015).

(1) Class I (UCLL): linear one-chain peptides (e.g. LL-37 and magainins) or two linear peptides not connected via a covalent bond (e.g. enterocin L50).

(2) Class II (UCSS): sidechain-sidechain linked peptides (e.g. disulfide-containing defensins or ether bond-containing lantibiotics). A sidechain-sidechain connection can occur within a single peptide chain or between two different peptide chains.

(3) Class III (UCSB): polypeptide chains with a sidechain to backbone connection (e.g. bacterial lassos and fusaricidins).

(4) Class IV (UCBB): circular polypeptides with a peptide bond between the N- and C-termini (i.e., backbone-backbone connection). Circular peptides have been found in bacteria (e.g.

), plants (e.g. cyclotides), and animals (e.g. theta-defensins).

For an update of this classification, please refer to Wang G (2022).

6. Based on 3D structure

In the Wang-edited book, AMPs are classified into four families: α, β, αβ, and non-αβ based on the types of secondary structures. The alpha family consists of AMPs with helical structures (e.g. magainins and LL-37). The beta family is composed of AMPs with beta-strands (e.g. human alpha-defensins). While the alphabeta family comprises both helical and beta-strands in the 3D structure (e.g. beta-defensins), the non-alphabeta family contains neither helical nor beta-strands (e.g. indolicidin). These four families of AMP structures are represented in the main page of this database . They are:

(1) frog magainin 2, alpha-helical (top left, PDB entry 2MAG);

(2) lactoferricin B, beta-sheet (top right, PDB entry 1LFC);

(3) plant defensin Psd1, αβ structure (bottom left, PDB entry 1JKZ);

(4) bovine indolicidin, non-αβ structure (bottom right, PDB entry 1G89). Note that non-αβ structures are broad and include all structures not covered by another three classes.

The numbers of AMPs with such structures are annotated in the APD and listed in the statistics.

7. Based on molecular targets

AMPs can be broadly classified into two families: cell surface targeting peptides (e.g. nisins and temporins) and intracellular targeting peptides (e.g. Pro-rich peptides). Cell surface-targeting peptides, including both membrane-targeting and non-membrane targeting peptides, can be further classified based on specific targets such as cell wall/carbohydrates, lipids/membranes, and proteins/receptors. Likewise, intracellular targeting AMPs can be further classified based on the specific target molecules (e.g. proteins, DNA, and RNA). Further details can be found in the Antimicrobal Peptide book below.


(1) Wang, G.(2022) Unifying the classification of antimicrobial peptides in the antimicrobial peptide database Methods in Enzymology 663, 1-18.

(2) Wang, G (2017) "Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies" (2nd version)CABI, England.

(3) Wang, G. (2015) Improved methods for classification, prediction, and design of antimicrobial peptides. Methods Mol. Biol. 1268, 43-66. PubMed.

Last updated: Jan 2024 | APD Copyright 2003-2024 Dept of Pathology, Microbiology and Immunology, UNMC All Rights Reserved