Frequently Asked Questions
How many natural antimicrobial peptides have been identified?
According to the antimicrobial peptide database, there are at least 2700 AMPs as of June 2016.
What is the Boman Index?
The Boman index was named by the APD database in 2003. 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 download it here. If the EXCEL format is preferred, you can email Dr. Wang at firstname.lastname@example.org.
Is it possible for us to predict a peptide sequence with more than 50 amino acid residues?
Yes, you can now.
Can we search for antimicrobial peptides from plants or bacteria 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). AMPs from different animals can also be searched (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, you can. 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).
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.
How do 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 (email: email@example.com). 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 June 2016, 111 AMPs contain the "provided by" tag, which can be searched in the "additional info" field.
The APD database is very helpful to my research. How do I cite it?
You can cite the following articles that describe the APD:
1. 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.
2. Wang, G., Li, X. and Wang, Z. (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research 37, D933-D937.
3. Wang, Z. and Wang, G. (2004) APD: the antimicrobial peptide database. Nucleic Acids Research 32, D590-D592.
If your search results are time dependent as a consequence of the regular database update, you can also indicate when the search was done and where you did the search:http://aps.unmc.edu/AP.