Construction and content phiBIOTICS database All data and information managed in phiBIOTICS were acquired manually from two main sources: (i) relevant research papers and books focused on identification and characterisation of enzybiotics and
their GM6001 concentration potential use as therapeutics and (ii) public databases (UniProtKB [18], Pfam [19], BRENDA [20]). The database back-end Ferrostatin-1 ic50 is built upon a free and open source software bundle, where MySQL (v4.0) is used as relational database management system. The web user’s interface of the database is developed in PHP programming language (v5.2.2) according to XHTML standard (1.0 Transitional). phiBiScan program utility Program module designated for search of potential enzybiotics is based on HMMER (v3.0) sequence homology
search software [21] ( http://hmmer.janelia.org/), which implements probabilistic hidden Markov models profile (HMMs). The database of HMMs is compiled of 16 profiles of protein domains/families with cell wall lytic activity and families/domains associated with this activity, obtained from the Pfam database v25.0 (Pfam entry names: Glyco_hydro_25, Amidase_2, Amidase_3, Amidase_5, Peptidase_M23, Glucosaminidase, VanY, CHAP, SLT, Phage_lysozyme, Phage_lysis, LysM, BAY 11-7082 supplier Glyco_hydro_19, Hydrolase_2, Peptidase_M15_3, Peptidase_U40). The selection of these domains was preceded with an extensive literature and database search. The database is compressed and indexed with hmmpress. To search sequences against profile database, hmmscan is used with default parameters. phiBiScan program utility is written in PHP, communication with the phiBIOTICS database is facilitated via SQL statements. Utility and discussion phiBIOTICS – catalogue of therapeutic enzybiotics Sclareol We have developed phiBIOTICS,
database of therapeutic enzybiotics, collecting information about all known and studied enzybiotics, relevant research studies and practical applications. Collected enzybiotics are mainly from bacteriophages, but also from other, bacterial sources. There are two basic requirements for including a new enzybiotic entry: (i) sequence has to be deposited in the UniProt database and (ii) there is publically available information about relevant research studies and/or practical applications. The database contains manually processed information about 21 enzybiotics and 69 corresponding research studies that represent currently known and studied enzybiotics. phiBIOTICS content is accessible via simple and intuitive user’s web interface at http://www.phibiotics.org/. Results of database browsing are divided into two main sections named: Enzybiotics Description and Relevant Studies. The schematic structure of database entries is shown in Table 1.