PMAP: databases for analyzing proteolytic events and pathways.
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.
Igarashi
Yoshinobu
Y
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.
Heureux
Emily
E
Doctor
Kutbuddin S
KS
Talwar
Priti
P
Gramatikova
Svetlana
S
Gramatikoff
Kosi
K
Zhang
Ying
Y
Blinov
Michael
M
Ibragimova
Salmaz S
SS
Boyd
Sarah
S
Ratnikov
Boris
B
Cieplak
Piotr
P
Godzik
Adam
A
Smith
Jeffrey W
JW
Osterman
Andrei L
AL
Eroshkin
Alexey M
AM
D030562:Databases, Protein; D006801:Humans; D053858:Metabolic Networks and Pathways; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D018511:Systems Integration
D011506:Proteins; D010447:Peptide Hydrolases