PRODORIC is an acronym for PROcariotIC Database Of Gene-Regulation (the term "doric" refers to greek columns, that's why there is a the greek temple on the home page). This database is an integrated approach to provide information about molecular networks in prokaryotes with focus on pathogenic organisms. In detail this concerns:
- transcriptional regulation (transcription factors and their DNA binding sites
- signal transduction (two-component systems, phosphylation cascades)
- protein interactions (complex formation, oligomerization)
- biochemical pathways (chemical reactions)
- other regulation events (e.g. codon usage, etc. ...)
In the long term it aims to be a resource to model protein-host interactions. Furthermore it will be a suitable platform to analyze high-throughput data from proteomis and transcriptomics experiments (systems biology).
Currently PRODORIC mainly contains detailed information about operon and promoter structures including huge collections of transcription factor binding sites. If an appropriate number of regulatory binding sites is available, a position weight matrix (PWM) and a sequence logo is provided, which can be used to predict new binding sites (see tools). This data is collected manually by screening the original scientific literature.
More recently PRODORIC was extended to handle protein-protein interactions and signal-transduction cascades that commonly occur in form of two-component systems in prokaryotes. Furthermore PRODORIC contains metabolic network data imported from the KEGG database.
not updated since 2008
May require some traning or trial and errors before mastering the tool.