A Brief Guide to the APD

1. Database Citations

Wang, Z. and Wang, G.* (2004) APD: the Antimicrobial Peptide Database (Abstract & PDF). Nucleic Acids Research 32, D590-D592.

Wang, G.*, Li, X. and Wang, Z. (2009) APD2: the updated antimicrobial peptide database and its application in peptide design (Abstract & PDF). Nucleic Acids Research 37, D933-D937. Invited.

2. Database Scope

The antimicrobial peptide field is growing rapidly in response to the demand for novel antimicrobial agents and the desire to understand their functions in innate immunity and its relationship with adaptive immunity and other systems. To promote the research, education, and information exchange in the field, we have created this antimicrobial peptide database and data analysis system, which we abbreviated as the APD. The data stored in the APD were gleaned from the Protein Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library of Medicine. The peptides in this database are in the mature and active form and primarily from natural sources, ranging from bacteria, fungi, plants, to animals. A few synthetic peptides of interest are also included. Antimicrobial proteins with more than 100 residues are not collected at this stage.

3. Database Capabilities

As an online E-dictionary, you can search the database for the detailed information of any antimicrobial peptide of interest in the following ways.
1. Structural features such as alpha-helix, beta-sheet, richness in unusual amino-acid residue, disulfide bond;
2. Peptide name or sequence;
3. Peptide family name such as cathelicidin;
4. Species name such as frog, toad, fish, and dog;
5. Original location: PDB, SwissProt or Reference;
6. Net charge: <0, =0 or >0;
7. Hydrophobic percentage;
8. Size;
9. Sequence motifs: e.g. finding all peptides containing sequences "M" or "DP";
10. Methods for structure determination: NMR spectroscopy, X-ray diffraction, or CD ;
11. Peptide posttranslational modification (codes are given in Abbreviations and citation 2);
12. Peptide binding partners (codes are given in Abbreviations or see citation 2);
13. Authors in the references;
14. AMPomics (Oct 14, 2009), i.e. all AMPs from a specific species, searched using its scientific name (e.g. Rana temporaria);
15. Additional info search (e.g. synergistic effect using syner;
16. Any combination of two or more options above.

The database also has the Prediction and Design Interfaces. The peptide prediction program allows you to input peptide sequence. The system will then traverse the database and do pairwise sequence alignment. The APD will then list several sequences that are most similar to your input. The program will calculate a similarity score and displays the differences between the input and stored sequences.

You can improve the activity of the peptide you designed based on the alignment results. You can also design novel peptides by using the sequence motifs (which can be obtained via the sequence search interface) found within the database (for examples, see the 2009 paper in the citations above).

This database also provides statistical information on peptide sequence, structure and function of all entries or a group of peptide entries of similar properties such as anticancer or from the same sources such as bacteria. The highly used amino acids (~>10%) in antimicrobial peptides from bacteria, plants, insects, and amphibians have been reported (see the 2009 paper above). This provides yet another approach for peptide engineering.

Some other databases related to antimicrobial peptides can be accessed via the Links. A brief discussion of those databases is given in a recent review article (Wang, G. 2007. Tool developments for structure-function studies of host defense peptides (Abstract) Protein Peptide Letters 14, 57-69).

For the definition of Boman index or protein-binding potential, as well as some abbreviations, please go to Glossary.

For selected papers contributed by the Wang Laboratory, please go to Selected Publications.

4. Database History, Update and Further Developments

This antimicrobial peptide database (APD) was originally created by a graduate student, Zhe Wang, as his Master thesis under the direction of Dr. Gus Wang. The first version of the database, open to the public in August 2003, contained 525 peptide entries. Some results were reported in the 2004 paper above.

The second version of our database (APD2) now contains 1518 antimicrobial peptides. For a summary of the developments and findings, see the 2009 paper above.

We apprecaite users who have emailed us their suggestions, corrections, or additions. We were able to incorporate such suggestions in the second version. While we are further developing the APD, you are welcome to email us your comments or suggestions. If your AMPs isolated from natrual sources are not found in the APD, please let us know by contacting us.

Version 1: Zhe Wang and Guangshun Wang* (2004);

Version 2: Guangshun Wang*, Xia Li, and Zhe Wang (2009)

Disclaimer: We do not assume liability for any claim due to the use of the APD or its derivatives. This page display is unnormal when the newest version Firefox 3 is used.