PMAP: databases for analyzing proteolytic events and pathways

Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak (+4 others)
2008 Nucleic Acids Research  
The Proteolysis MAP (PMAP, http://www. proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, Protease-DB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic 'Molecule Pages', rich in molecular information. PMAP also contains two community annotated databases focused on function;
more » ... utDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition specificity of proteases. Together, the content within these four databases will ultimately feed PathwayDB, which will be comprised of known pathways whose function can be dynamically modeled in a rule-based manner, and hypothetical pathways suggested by semi-automated culling of the literature. A Protease Toolkit is also available for the analysis of proteases and proteolysis. Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis.
doi:10.1093/nar/gkn683 pmid:18842634 pmcid:PMC2686432 fatcat:kp24qbe6vjhmfdsqvhhswibbcu