pfba-lab-tun.org/links.php. The AMSDb (see: check details http://www.bbcm.univ.trieste.it/~tossi/amsdb.html), ANTIMIC [18], APD2 [19], and CAMP [20] databases cover all AMPs sequences from diverse origins. Alternatively, some databases focus on AMPs produced by bacteria (BACTIBASE [8]), plants (PhytAMP [21]) and shrimp (PenBase [22]). While AMSdb database covers only AMPs of eukaryotic origin, ANTIMIC database contains about 1700 AMPs from diverse origins (eukaryotes, prokaryotes). Regrettably, this resource was discontinued. The Antimicrobial Peptide Database (APD2) is the most popular of the currently available
public collections (containing 944 antibacterial peptides of eukaryotic and prokaryotic origin) [19]. Recently, a new database containing a large Collection of Anti-Microbial Peptides (CAMP) was developed and holds 3782 antimicrobial sequences [20]. While lantibiotics are the class I of bacteriocins, the CAMP database lists them as a distinct family from bacteriocins. This may confuse novice users. Although APD2 and CAMP databases contain very LCZ696 price general information about peptides of all types having antibacterial, antifungal or antiviral activities and originating from either eukaryotic or prokaryotic cells, bacteriocins are not described with a useful amount of detail in either of these databases. Not only does BACTIBASE (version 2, July 2009) contain significantly
more antimicrobial peptides of bacterial origin, than the APD2 and CAMP databases (177 in BACTIBASE versus ~120 in APD2 and ~68 in CAMP), but also every entry in BACTIBASE is much more detailed. BACTIBASE features, for example, physicochemical and structural information, detailed lists of target organisms and a description of the mode of action for each bacteriocin — data not available in APD2 or any other online resource (to the best of our knowledge). Also, BACTIBASE next hosts a rich and highly usable collection of references, where (i) each entry has been supplied with a short annotation summarizing its topic in
~10 words or less, (ii) is cross-linked to PubMed, and (iii) can be conveniently exported to LY3023414 clinical trial Citation Manager Software of user’s choice. The database provides several tools for bacteriocin sequence analysis (unavailable in APD2; unavailable or static in CAMP), such as homology search, multiple sequence alignments, Hidden Markov Models and molecular modeling. All this makes BACTIBASE a truly unique resource for bacteriocins. Future directions We are currently developing a system for automatic updating of the database. New types of data will be added in the near future. Subsequent development will include integrating a system that automates the prediction of bacteriocin functional amino acids as well as enriching the platform with useful tools for bacteriocin characterization. We also hope to develop new methods/techniques for structural and functional classification of bacteriocins.