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APD / Antimicrobial Peptide Database

Focuses on natural antimicrobial peptides (AMPs) with defined sequence and activity. APD includes a total of 2619 AMPs with 261 bacteriocins from bacteria, 4 AMPs from archaea, 7 from protists, 13 from fungi, 321 from plants and 1972 animal host defense peptides. The APD3 contains 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic and 185 anticancer peptides. Newly annotated are AMPs with antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties. A unique and powerful feature of the APD3 is that its search interface consists of a pipeline of search functions. The more one selects or enters, the less one will get. Without activating anything in the interface, a simple search returns all the peptides in the database. The users can filter the information freely at their will. To make it more convenient, the APD3 has enhanced the search interface by re-grouping the existing search icons into functional zones based on information types and by adding new search icons for peptide activity.

CAMP / Collection of Anti-Microbial Peptides

A database of sequences, structures and family-specific signatures of prokaryotic and eukaryotic antimicrobial peptides (AMPs). Family-specific sequence signatures comprising of patterns and Hidden Markov Models were generated for 45 AMP families by analysing 1386 experimentally studied AMPs. These were further used to retrieve AMPs from online sequence databases. More than 4000 AMPs could be identified using these signatures. AMP family signatures provided in CAMPR3 can thus be used to accelerate and expand the discovery of AMPs. CAMPR3 presently holds 10247 sequences, 757 structures and 114 family-specific signatures of AMPs. Users can avail the sequence optimization algorithm for rational design of AMPs.

SATPdb

A collection of therapeutically important peptides from different peptide databases/datasets. These peptides were curated and classified based on their major function, therapeutic property and sub-function. The current version holds 19192 unique experimentally validated therapeutic peptide sequences having length between 2 and 50 amino acids. It covers peptides having natural, non-natural and modified residues. These peptides were systematically grouped into 10 categories based on their major function or therapeutic property like 1099 anticancer, 10585 antimicrobial, 1642 drug delivery and 1698 antihypertensive peptides. Briefly, users can take advantage of SATPdb in following ways: users can (i) search a peptide of interest in 22 peptide databases/datasets at one go and therefore save time, (ii) browse peptides of SATPdb with similar physicochemical properties or secondary structure content, (iii) extract moonlighting peptides with desired functions and (iv) extract structural information of most of the peptides including peptides with non-natural residues which can be used for further structure-to-function analysis and docking studies.

DBAASP / Database of Antimicrobial Activity and Structure of Peptides

Obsolete
A manually curated database for those peptides for which antimicrobial activity against particular targets has been evaluated experimentally. The database is a depository of complete information on: the chemical structure of peptides; target species; target object of cell; peptide antimicrobial/haemolytic/cytotoxic activities; and experimental conditions at which activities were estimated. The DBAASP search page allows the user to search peptides according to their structural characteristics, complexity type (monomer, dimer and two-peptide), source, synthesis type (ribosomal, nonribosomal and synthetic) and target species. The database prediction algorithm provides a tool for rational design of new antimicrobial peptides.

ANTISTAPHYBASE

Facilitates the access to important information on antimicrobial peptides (AMPs) and essential oils (EOs) against Methicillin-resistant S. aureus (MRSA) and Staphylococcus aureus. ANTISTAPHYBASE is a database that permits a quick and easy search of peptides on the base of their activity as well as their general, physicochemical properties and literature data. These characteristics are all very useful to perform further bioinformatics or chemometric analysis and would certainly be useful for the development of new drugs for medical use.

DAMPD / Dragon Antimicrobial Peptide Database

Obsolete
An update and a replacement of the ANTIMIC database. In DAMPD an integrated interface allows in a simple fashion querying based on taxonomy, species, antimicrobial peptide (AMP) family, citation, keywords and a combination of search terms and fields (Advanced Search). A number of tools such as Blast, ClustalW, HMMER, Hydrocalculator, SignalP, AMP predictor, as well as a number of other resources that provide additional information about the results are also provided and integrated into DAMPD to augment biological analysis of AMPs.

MAHMI / Mechanism of Action of the Human Microbiome

Provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. It provides researchers with a comparative tool for inspecting the potential immunomodulatory or antiproliferative bioactivity of new amino acidic sequences and identifying promising peptides to be further investigated.

BaAMPs

A database dedicated to antimicrobial peptides (AMPs) specifically tested against microbial biofilms. The aim of this project is to provide useful resources for the study of AMPs against biofilms to microbiologist, bioinformatics researcher and medical scientist working in this field in an open-access framework. In BaAMPs, information related to AMP sequence, chemical modifications, associated with target organisms, experimental methods, peptide concentration and percentage of biofilm inhibition/reduction, are manually extracted and curated from literature. Furthermore, peptides and experimental data are linked to the DOI of the related original article, allowing users to reach the on-line article page. Thanks to its sleek and intuitive web interface, users can rapidly query and retrieve information on AMPs/biofilms according to the desired search criteria.

BACTIBASE

Stores calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. BACTIBASE is a relational database that aims to serve the research community by organizing information relevant to all types of bacteriocins from all groups of Bacteria. Several useful tools for protein analysis are integrated into the platform. The database should be useful for discovering and characterizing potent bacteriocins or designing novel peptides with greater antimicrobial activity against pathogens.