Appl Bioinformatics 2005; 4 (2): 147-150 APPLICATION NOTE 1175-5636/05/0002-0147/$34.95/0  2005 Adis Data Information BV. All rights reserved. ProLysED An Integrated Database and Meta-server of Bacterial Protease Systems Mohd Firdaus Raih, 1,2 Hafiza Aida Ahmad, 2 Mohd Yunus Sharum, 2 Norazah Azizi 2 and Rahmah Mohamed 1,2 1 School of BioSciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia 2 Malaysia Genome Institute, Universiti Kebangsaan Malaysia - Malaysia Technology Development Corporation (UKM-MTDC) Smart Technology Centre, Bangi, Malaysia Bacterial proteases are an important group of enzymes that have very diverse biochemical and cellular Abstract functions. Proteases from prokaryotic sources also have a wide range of uses, either in medicine as pathogenic factors or in industry and therapeutics. ProLysED (Prokaryotic Lysis Enzymes Database), our meta-server integrated database of bacterial proteases, is a useful, albeit very niche, resource. The features include protease classification browsing and searching, organism-specific protease browsing, molecular information and visual- isation of protease structures from the Protein Data Bank (PDB) as well as predicted protease structures. Availability: ProLysED is integrated into the ProLysES (Prokaryotic Lysis Enzymes Site) website at http:// genome.ukm.my/prolyses/. Access to the ProLysED database is free for academic users upon registration. Contact: M. Firdaus Raih (prolysed@cgat.ukm.my or mfirr@pkrisc.cc.ukm.my) Proteases are a class of enzymes that catalyse the cleavage of analysis and related information will enable refinement of current peptide bonds in other proteins. Proteases have had a long history work on bacterial proteases, as well as assist in generating new of applications in the food, detergent and leather industries. These knowledge on bacterial proteases in general, be it for industrial proteins also represent one of the three largest groups of industrial applications, pharmaceuticals or academic research. enzymes and account for up to 60% of the total worldwide sale of The resulting database, ProLysED (Prokaryotic Lysis Enzymes enzymes. [1] Bacterial proteases have a diverse range of function Database), was not intended to be an extensive exploration into and mechanisms of action. They can be responsible for complex proteolytic enzymology as a whole, such as the MEROPS processes under normal physiological circumstances as well as in database. [2] It was instead targeted as a niche resource in prokary- abnormal patho-physiological conditions. otic protease systems, which may include non-proteolytic associ- Current advances in DNA sequencing technology have made ated datasets. An existing resource, which similarly explores a available a large number of unannotated and as yet unstudied niche protease dataset, is the HIV Protease Database (http:// datasets alongside well studied and well characterised models. mcl1.ncifcrf.gov/hivdb/). This archive is more focused on a These datasets, when integrated with current extrapolative tools dataset sourced from HIV-related crystallography experiments. In and used in conjunction with well studied models, can yield useful this article we report on the ProLysED database, which is dynami- information, which can then be used for comparative analysis cally annotated, covering a dataset of bacterial protease systems. leading to the laboratory refinement of experiments. We set out to ProLysED is further enhanced by the use of a meta-server to make use of publicly available data on bacterial proteases for this provide constantly updated information by cross-referencing other purpose by adding value to information in these datasets and relevant data resources, including the MEROPS database of Rawl- organising it into an integrated meta-server interface for electronic ings et al. [2] access and analysis. It is hoped that the resulting comparative