A Brief Guide to the APD
1. Database scope
The antimicrobial peptide (AMP) field is growing rapidly in response to the demand for novel antimicrobial agents for drug-resistant pathogens such as superbugs, viruses, fungi, and parasites, as well as 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 retrieval 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, Google, and Swiss-Prot) manually in the past several years.
Peptides will be registered into this database if
(1). they are from natural sources (bacteria, protozoa, fungi, plants, and animals);
(2). antimicrobial activities are demonstrated (MIC <100 uM or 100 ug/ml);
(3). the amino acid sequences of the mature peptides have been elucidated, at least partially; and
(4). antimicrobial peptides contain less than 100 amino acid residues (Starting October 2012, the APD database also includes some small yet important antimicrobial proteins <200 aa).
Although not the focus of this database, a few synthetic peptides of interest (~2% of the entries) are collected as separate entries. However, additional synthetic peptides derived from natural AMPs are annotated in their parent entries as Derivative or Variants to enhance info correlation and to optimize sequence uniqueness in this database.
2. Database capabilities and AMP sub-databases
Our goal is to develop the antimicrobial peptide database into a comprehensive tool for discovery timeline, naming (nomenclature), classification, information search, statistical analysis, prediction, and design of antimicrobial peptides covering all life kingdoms (bacteria, protozoa, fungi, plants, and animals). As an online E-dictionary, you can search the database
for detailed info for any peptide (using the standard 20 aa) 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, cattle, 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 more 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
(10). Cationic or anionic AMPs based on the net charge: <0, =0 or >0;
(11). Hydrophobic residue
(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 or year of publication 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 (search with fungii), 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, spiders, etc).
The database also has the Prediction and Design Interfaces.
The APD database has a unique peptide prediction program. After you input the sequence, the program will calculate select properties of the peptide (e.g. net charge, length, hydrophobic residue% and amino acid composition). If the calcualted pamameters are out of the APD-defined space for natural AMPs, the program will stop (Nov 2013 version). Otherwise, the system will traverses the
database and does pairwise sequence alignment. The APD will then list
five peptide 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.
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. Examples of statistic data about AMPs can be viewed here.
For additional information, please visit other websites in the Links.
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.
For frequently asked questions from users, please refer to the FAQ page.
Selected peptide parameters and properties can be calcualted using the peptide calculator of the APD. In addition, the APD has also generated my tools page for users to calculate other properties of newly discovered AMPs.
3. Database history, update and further development
The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his Master thesis in the laboratory 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, amino acid sequence, 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 database paper.
The second version of our database (APD2) reported 1228 antimicrobial peptide entries. Major features added are peptide source, family, chemical modifications, and binding targets. A summary of the new developments and database findings is described in the 2009 database paper. New web design is credited to Sophie Wang.
Since then, the database has been further updated and expanded. New web pages for FAQs, interesting AMP discovery timeline, classification, and nomenclature have been created. As of May 2014, the current AMP database contains over 2400 antimicrobial peptides and proteins, 98.5% 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 (e.g. Erik Martin and Biswajit Mishra). While we are further developing this database, you are welcome to make contributions. If your new AMPs isolated from natural sources escaped our attention, please
Disclaimer: Although every effort is made to make the database as complete and accurate as possible, we do not assume
liability for any claim due to the use of the APD or its derivatives.