Frequently Asked Questions

How many natural antimicrobial peptides have been identified with known activity?

According to the antimicrobial peptide database, there are 3146 natural AMPs with known antimicrobial activity as of Dec 2023. This list has been refined recently and does not include natural peptides without antimicrobial activity.

What is the Boman Index?

The Boman index was named by the APD database in 2003 in honor of Hans Boman. It was originally called "protein-binding potential" by Hans Boman. The Boman index is the sum of free energies of the respective side chains for transfer from cyclohexane to water, taken from Radzeka and Wolfenden, and divided by the total number of the residues of an antimicrobial peptide. The calculated values are negative (except for the hybrid peptide), but the + and - are reversed [Boman, H.G. (2003) J. Inter. Med. 254:197-215].

Can we get a list of antimicrobial peptide (AMP) sequences in the FASTA format?

Yes, you can search and download all or part of the peptide sequences in the FASTA format. If the EXCEL format is preferred, you can email Dr. Wang at

Is it possible for us to calculate and predict a peptide sequence with more than 50 amino acid residues?

Yes, you can.

Can we search for antimicrobial peptides from bacteria, plants, or animals only?

Yes, you can do this by entering "plants" into one of the search boxes in the NAME field. Then you can search for the info in the usual way. Likewise, you can search for a list of AMPs from bacteria (i.e. bacteriocins) or a vareity of animal classes (see About).

How do I obtain a list of AMPs that bind to lipopolysaccharides (LPS) or endotoxin?

You can search for such peptides by entering the code "BBL" into one of the search boxes in the NAME field. For additional codes for AMP-binding partners, go to the Glossary page.

Can I search for AMPs in the form of dimer or two chains?

Yes, you can do so by entering "dimer" or "two-chain" into the NAME field followed by database search.

Can I search for AMPs based on the year of publication?

Yes. This function currently shares the same search box with the author search. A plot of AMPs discovered annually can be found online here (Wang, G. 2013 Pharmaceuticals 6: 728-758). Based on the most recent plot for natural AMPs in the APD, the antimicrobial peptide research may be classified into three major phases. Phase 1 started with the discovery of lysozyme in 1922. The second phase started in the 1980s due to the clear growth of natural AMPs. The third phase is defined as the omics era since the completion of sequencing of human genome in 2003 (Protein Sci).

Does the database contain a link to the PubMed for each peptide entry?

Yes, this has been enabled for new entries and the links for the old entries are under construction. Additional references are anotated in the "Additional Info" field, which is under constant reformatting..

How can I submit my peptides to the APD database?

We appreciate your input. The easiest way is to email Dr. Wang a copy of your article after publication (email: In particular, we encourage you to include your peptide sequences in your email. This will minimize potential errors during data registration. The APD acknowledges your contributions by including "provided by YOU" in each entry. As of Jan 2024, users and friends have assisted with the registration of 288 AMPs in the APD.

How can I search machine learning predicted peptides?

Recently, a new peptide group "predicted" has been established in the APD to reflect the rapid development of AI prediction of antimicrobial peptides. You can search such peptides in the name field using "predicted" (Protein Sci 2023).

How can I search antimicrobial peptides discovered from microbiota?

The APD first included this info in the field for Source organism (Protein Sci 2022). You can search "microbiota" there. Thew biological source can be appended behind to do the same search, e.g., microbiota:gut or microbiota:skin.

The APD is very helpful to my research. How do I cite it?

You can cite the following articles that describe the APD:

Wang, G, Li, X. and Wang, Z.(2016) APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Research 44, D1087-D1093.

If your search results are time dependent as a consequence of the regular database update, you can also indicate when the search was done as required by some journals.

Last updated: Jan 2024 | Copyright 2003-2024 Dept of Pathology, Microbiology and Immmunology since 2023, UNMC All Rights Reserved