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PMAP: databases for analyzing proteolytic events and pathways

The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
Nucleic Acids Research (Impact Factor: 9.11). 11/2008; 37(Database issue):D611-8. DOI: 10.1093/nar/gkn683
Source: PubMed

ABSTRACT 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, ProteaseDB 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; CutDB 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.

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Available from: Alexey M Eroshkin, Aug 31, 2015
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    • "PMAP-CutDB b http://www.proteolysis.org/proteases/ Jeffrey Smith H, M, R, A, D, C Igarashi et al. 2009 MEROPS b http://merops.sanger.ac.uk/index.shtml Neil Rawlings & Alan Barret H, M, R, A, D, C Rawlings et al. 2012 are claimed to have for individual caspases in whole cell and in vivo assays where multiple caspases are present (Garcia-Calvo et al. 1998; Ekert et al. 1999), as well as in some in vitro assays (Berger et al. 2006b; McStay et al. 2008; Pereira and Song 2008; Benkova et al. 2009). "
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    • "However, this database does not easily allow a user to perform specific meta-analyses such as a direct comparison among substrates. PMAP/CutDB on the other hand is a community-driven (Wikipedia style) database, implying that any scientist can add new substrates or substrate predictions (15,16). The intrinsic disadvantage is that the quality of the reported substrates cannot be guaranteed, especially because the original data leading to the discovery of a substrate can only be accessed by using the provided links to the original article. "
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