Wang, Z. and Wang, G. (2004) APD: the Antimicrobial Peptide Database (Abstract). Nucleic Acids Research 32, D590-D592.
Antimicrobial peptides, also referred to as host defense peptides or "alarmins", have been identified in nearly all life forms, ranging from bacteria, fungi, plants, insects, amphibians, to mammals, including humans. As the key component of the innate immunity, these ancient peptides effectively eliminate invanding microbes such as bacteria, viruses, fungi, and parasites. It is commonly believed that antimicrobial peptides exert their effects via attacking bacterial membranes. Currently, there is high interest worldwide in this topic with a goal of understanding the mechanism of action and developing natural antimicrobial peptides into a new generation of antibiotics. To promote the research, education, and information exchange in the field, we have created this antimicrobial peptide database and data analysis system. 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 form and primarily from natural sources ranging from bacteria, plants, to animals. For example, amphibians are a well-known source for antimicrobial peptides and 385 entries out of 1000 are stored in the APD till August 2008. Some synthetic peptides of particular interest to the research community are also considered. Antimicrobial proteins with more than 100 residues will not be collected at this stage.
As an online dictionary, users can search the database for the detailed information of any antimicrobial
peptide of their 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 or X-ray diffraction. CD (under construction). Representative 3D structures for antimicrobial peptides can be viewed at the entrance page of
the APD;
11. Any combination of two or more options above.
The APD also provides useful tools for database mining. Based on the database, some common features of antimicrobial peptides have emerged and reported (for details, please refer to the citation above).
The database also has the Prediction and Design Interfaces. Since the amino acid sequence determines the activity of the peptide, sequence similarity suggests structural and functional similarities. This program allows users to input their own peptide sequence. The system will then traverse the database and do sequence alignment. The APD will do pairwise alignments and list several sequences that are most similar to user's input. The system will calculate the similarity score and show the differences between the input sequence and stored sequences. When users want to design a new antimicrobial peptide, they can improve the therapeutic index of their peptide based on the alignment results. Users can also design novel peptides by using the sequence motifs found within the database.
This database also provides Statistical Information on peptide sequence, structure and function. This provides yet another approach for peptide engineering.
Some other related databases 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, please go to Glossary and click on the icon host defense peptides. Some Abbreviations used in the APD are also listed.
For selected papers contributed by the Wang Laboratory, please go to Selected Publications.
This antimicrobial peptide database (APD) was originally created by a graduate student, Zhe Wang, as his Master thesis under the support and guidance of Dr. Gus Wang. When the database was made available to the public in August 2003, there were 525 peptide entries (see the citation above). After the update during 2007 and 2008 by Dr. Gus Wang, the APD now contains more than 1200 antimicrobial peptide entries. In addition, users can now search the database using peptide family names or species names. Our goal is to make the peptide entries as accurate and complete as possible. You are welcome to email your newly discovered peptides to us, or making suggestions by contacting us.
Acknowledgements: We thank Joe Ziskovsky and Atul Rayamajhi for consistent support to make it accessible by users via web.
Disclaimer: The database is provided as it is and we do not assume liability for any loss due to the use of the APD.
By Zhe Wang, Xia Li, and Gus Wang, last modified on Sept. 2, 2008.