A Brief Guide to the APD

1. Database Citations

Wang, Z. and Wang, G.* (2004) APD: the Antimicrobial Peptide Database (Abstract & paper). 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 & paper). Nucleic Acids Research 37, D933-D937. Invited.

2. Database Scope

The antimicrobial peptide (AMP) field is growing rapidly in response to the demand for novel antimicrobial agents for resistant microbes and our desire to better understand the functions of AMPs in innate immunity and their relationship with adaptive immunity and other biological systems. To promote the research, education, and information exchange in the field, we created, and have been updating and expanding, the Antimicrobial Peptide Database and data analysis system, which we abbreviated as the APD. It is a system dedicated to glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs and beyond. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, and Swiss-Prot) manually in the past several years. Peptides will be registered into this database if

(1). they are from natural sources (bacteria, fungi, plants, and animals);

(2). their antimicrobial activities are known (MIC <100 uM or 100 ug/ml);

(3). their amino acid sequences have been elucidated, at least partially;

(4). the mature peptides contain less than 100 amino acid residues.

In addition, some synthetic peptides of interest (~2% of the entries) are collected as separate entries. However, additional synthetic peptides derived from natrual AMPs are annotated in their parent entries to enhance info correlation and to optimize the sequence uniqueness in this database.

3. Database Capabilities and AMP Subdatabases

Our goal is to develop the antimicrobial peptide database into a useful tool for naming (nomenclature), classification, information search, statistical analysis, prediction, and design of antimicrobial peptides. As an online E-dictionary, you can search the database for detailed info for any AMPs of interest in many ways as listed below.

(1). Peptide full sequence, partial sequence, or motifs in the single-letter amino acid code such as DP and ILIKEAPD;
(2). In the name field, peptide name such as magainin, thanatin, gomesin, kalata B1, cecropin, aurein 1.2, dermaceptin;
(3). Peptide family name such as defensin, cathelicidin, and histatin;
(4). Common name for peptide source species such as human, cow, frog, fish, spider, snake, and fungii (actual search words);
(5). Kingdom name for peptide sources such as protozoan, bacteria, archaea, fungii, plants, and animals;
(6). Peptide post-translational modification using search keys such as XXA (amidation), XXC (cyclization), XXD (D-amino acids), XXE (N-terminal acetylation), XXG (glycosylation), XXH (halogenation), XXK (hydroxylation), XXO (oxidation), XXP (phosphorylation), XXQ (N-terminal cyclic glutamate), and XXS (sulfation); A complete list can be downloaded here.
(7). Peptide-binding partners or targets using search keys such as BBS (carbohydrates), BBL (lipopolysaccharides, LPS, endotoxin) and BBII (cations such as Zn2+), BBN (nucleic acids), BBMm (biological membranes) (listed in the Glossary);
(8). Still in the name field, AMPs with insecticidal, anti-parasital, spermicidal effect can be searched by using ZZI, ZZP, and ZZS, respectively (NOTE that you can view AMPs with such activities DIRECTLY in the MAIN.php page;
(9). Peptide original location: PDB, SwissProt or Reference;
(10). Cationic or anionic AMPs based on the net charge: <0, =0 or >0;
(11). Hydrophobic residue percentage;
(12). Peptide length (Size);
(13). Biophysical methods for structure determination: NMR spectroscopy, X-ray crystallography, or Circular Dichroism (CD) ;
(14). Structural features such as alpha-helix, beta-sheet, richness in unusual amino-acid residues (i.e. Pro and Trp, or disulfide bonds);
(15). Authors in the references;
(16). In the biological activity field, antibacterial (Gram-positive only or Gram-negative only), antiviral, antifungal, and anticancer peptides or AMPs with a cytotoxic effect on mammalian cells (usually hemolysis);
(17). Source species search in scientific name (e.g. Homo sapiens). This allows for the search of all AMPs from a specific living species so far collected into the APD.
(18). In the Additional info field, synergistic effect using syner;
(19). MOA (mechanism of action) in the Additional info field; and
(20). Any combination of two or more options above.

In addition, the annotation in the NAME field allows users to search AMP information from a specified life kingdom or domain such as bacteria, fungi, plants, and animals. For example, a subdatabase for bacterial AMPs can be generated by entering the word "bacteria" into one of the search boxes in the name field, and any properties of the bacterial AMPs (i.e. bacteriocins) can be searched in the usual way. Likewise, users can search AMPs from plants or animals (amphibians, fish, reptiles, birds, insects, spiders, mollusks, worms, crustacea, etc).

The database also has the Prediction and Design Interfaces. The peptide prediction program allows you to input peptide sequence. The program will calculate select properties of the input peptide such as net charge, peptide length, hydrophobic residue% and other amino acid compositions. The system also traverses the database and does 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).

The APD 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. Such bioinformatics analyses have led to the identification of the frequently used amino acids (~>10%) in antimicrobial peptides from a defined life kingdom, peptide family, or group such as bacteria, plants, insects, amphibians, defensins, cyclotides, and lantibiotics. These residues have been utilized for de novo design of novel AMPs (see the 2009 paper above).

For additional information, please visit other websites in the Links. A brief discussion of the related AMP databases is given in a review article (Wang, G. 2007. Tool developments for structure-function studies of host defense peptides (Abstract) Protein Peptide Letters 14, 57-69). For an updated description, please refer to the Antimicrobial Peptide book (edited by Wang, G., 2010).

For the definition of selected terms related to AMPs, 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. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 paper above.

The second version of our database (APD2) reported 1228 antimicrobial peptide entries. Major features added are peptide source, family, chemical modifications, and binding tagets. A summary of the new developments and database findings is discussed in the 2009 paper above.

Since then, the database has been further updated and expanded. New web pages for FAQs and AMP chronicle have been added. As of March 2012, the current APD contains >1960 AMPs, primarily from living prokaryotic and eukaryotic cells.

We appreciate users who have emailed us their suggestions, corrections, or additions. We were able to incorporate them in the second version and gave credits by including the provider's name in the related entries. While we are further developing the APD, you are welcome to make suggestions. If your new AMPs isolated from natural sources are absent in the APD, please contact us.

Disclaimer: Although we do not assume liability for any claim due to the use of the APD or its derivatives, users should acknowledge the use of, or extraction of data from, this database.