A Brief Guide to the APD
1. Database scope
Antimicrobial peptides (AMPs), or host defense peptides, are essential components of innate immune systems. A natural name for AMPs can be innate immune peptides, which not only eliminate invading pathogens rapidly (faster than bacterial replication) but also initiate additional immune responses to further clean up the system. The antimicrobial peptide field is growing rapidly in response to the demand for novel antimicrobial agents for drug-resistant pathogens such as superbugs, viruses, fungi, and parasites. There is also the 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 and knowledge discovery in the field, we created, and have been updating and expanding,
the Antimicrobial Peptide Database and data analysis system, which is 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 over a decade. To have a clean set of data, the APD first set up criteria for data registration.
Peptides will be registered into this database if
(1). they are from natural sources (three domains or six kingdoms);
(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 >100 aa).
Although not the focus of this database at present, 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.
In the same spirit, AMPs from different species but sharing the same peptide sequence occupy one entry in the APD3 (search using "found in multiple species" in the Additional Info field).
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 six life kingdoms (bacteria, archaea, protists, 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). peptide sources, e.g. three domains (bacteria, archaea, eukaryotes) or six kingdoms (bacteria, archaea, protists, 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). Still in the name field, AMPs that form dimers can be searched by entering "dimer" (hetero or homo);
(8). 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);
(9). Peptide original location: PDB, SwissProt or
(10). Cationic, neutral, or anionic AMPs based on the net charge: <0, =0 or >0;
(11). Hydrophobic residue content (Pho%);
(12). Peptide length (size);
(13). Biophysical methods for structure determination: NMR spectroscopy, X-ray crystallography, or Circular Dichroism (CD);
(14). Structural classification such as alpha-helix, beta-sheet, alphabeta, or non-alphabeta;
(15). Contributing authors or year of AMP publication in the references;
(16). In the biological activity field, antibacterial (Gram-positive only or Gram-negative only), antiviral, antifungal, and anticancer peptides.It appears that AMPs have multiple functions, which the APD continues to add with time;
(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, archaea, 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, invertebrates, insects, spiders, mollusks, worms, crustacean, 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 calculated parameters 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 database
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 complementary information (e.g., additional synthetic or predicted AMPs), you can visit related websites in the Links.
For the definition of selected terms or abbreviations related to AMPs, 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 calculated 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's 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 2nd version of our database (APD2) reported 1,228 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. The new web design is credited to Sophie Wang.
The 3rd version of the APD (APD3) reported 2,619 peptides. New web pages for FAQs, interesting AMP discovery timeline, classification, nomenclature, AMP facts, My tools, Sequence download, and APD News have been created. A unified peptide classification system has been proposed and introduced. In addition, the prediction interface has been improved and additional peptide properties can be calculated.
The APD is regularly updated and annotated. As of Dec 2018, the current AMP database contains over 3,048 antimicrobial peptides and proteins from living prokaryotic and eukaryotic organisms.
We appreciate users who emailed us their suggestions, corrections, or additions. We were able to incorporate them in the current version and gave credits by including the provider's name in the related entries (e.g. T. Stein, Erik Martin, Adel Ghorani-Azam, Hadi Zare-Zardini, M. Bassam Alkotaini, Brice Felden, Sven-Ulrik Gorr). 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.