View source for The Proteolysis Map

{{Short description|Integrated web resource focused on proteases}}
{{Cleanup-PR|date=December 2019}}
[[Image:PMAP-logoV8-2blue.png|100px|thumb|right|'''PMAP logo''']]

'''The Proteolysis MAP''' ('''PMAP''') was an integrated [[web resource]] focused on [[protease]]s.<ref>{{cite journal | last1 = Igarashi | first1 = Y | last2 = Heureux | first2 = E | last3 = Doctor | first3 = KS | last4 = Talwar | first4 = P | last5 = Gramatikova | first5 = S | last6 = Gramatikoff | first6 = K | last7 = Zhang | first7 = Y | last8 = Blinov | first8 = M | last9 = Ibragimova | first9 = SS | last10 = Boyd | first10 = S | last11 = Ratnikov | first11 = B | last12 = Cieplak | first12 = P | last13 = Godzik | first13 = A | last14 = Smith | first14 = JW | last15 = Osterman | first15 = AL | last16 = Eroshkin | first16 = AM | year = 2008 | title = PMAP: databases for analyzing proteolytic events and pathways | journal = [[Nucleic Acids Research]] | volume = 37| issue = Database issue| pages = D611–D618| doi=10.1093/nar/gkn683 | pmid=18842634 | pmc=2686432}}</ref> Its domain now links to a scam/spam browser extender.

==Rationale==
PMAP was designed to aid the protease researchers in reasoning about [[proteolytic]] [[metabolic network|networks]] and [[metabolic pathways]].

==History and funding==
PMAP was originally created at the [[Burnham Institute for Medical Research]], La Jolla, California.  In 2004 the [[National Institutes of Health]] (NIH) selected a team led by [[Jeffrey W. Smith]], to establish the Center on Proteolytic Pathways (CPP).  As part of the NIH Roadmap for Biomedical research, the center develops technology to study the behavior of proteins and to disburse that knowledge to the scientific community at large.

==Focal point==
Proteases are a class of [[enzymes]] that regulate much of what happens in the [[human body]], both inside the [[Cell (biology)|cell]] and out, by cleaving [[peptide bonds]] in [[proteins]].  Through this activity, they govern the four essential cell functions: [[differentiation (cellular)|differentiation]], [[motility]], division and [[cell death]] — and activate important [[extracellular]] episodes, such as the [[biochemical cascade]] effect in [[blood clotting]]. Life could not exist without them. Extensive on-line classification system for proteases (also referred as peptidases) is deposited in the [[MEROPS]] database.

==Goal==
Proteolytic pathways, or proteolysis, are the series of events controlled by proteases that occur in response to specific stimuli.  The clotting of blood and production of [[insulin]] can be viewed as proteolytic pathways. The activation, regulation and inhibition of the protein are protease reactions to changing [[glucose]] levels and trigger other proteases downstream.

==Database content==
PMAP integrates five databases.
ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic 'Molecule Pages', rich in molecular information. CutDB<ref>Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A. CutDB: a proteolytic event database. [[Nucleic Acids Research]]. 2007 D546-9</ref> has information on more than 6,600 proteolytic events, and ProfileDB is dedicated to information of the [[Substrate (biochemistry)|substrate]] recognition specificity of proteases. PathwayDB has begun accumulation of [[metabolic pathways]] whose function can be dynamically modeled in a rule-based manner. Hypothetical networks are inferred by semi-automated culling from the literature. Protease software tools may help analyze individual proteases and [[proteome]]-wide datasets.

==Usage==
Popular destinations in PMAP are Protease Molecule Pages and Substrate Molecule Pages. Protease Molecule Pages show recent news in [[PubMed]] literature of the protease, known [[proteolytic events]], [[protein domain]] location and [[protein structure]] view, as well as a cross annotation in other [[bioinformatic]] databases section. Substrate Molecule Pages display protein domains and experimentally derived protease cut-sites for a given protein target of interest.

==See also==
* [[Cytoscape]]
* [[Computational genomics]]
* [[Metabolic network modelling]]
* [[Protein–protein interaction prediction]]

==References==
{{reflist}}

==External links==
* {{MeshName|Proteases}}
* [https://web.archive.org/web/20170420071011/http://sonny.burnham.org/proteases Official website]
* [https://web.archive.org/web/20110903233056/http://cutdb.burnham.org/ Proteolysis Cut Site database - curated expert annotation from users]
* [https://web.archive.org/web/20081222011039/http://substrate.burnham.org/ Protease cut sites graphical interface]
* [http://www.expasy.org/tools/peptidecutter/ Protease cutting predictor]
* [http://merops.sanger.ac.uk/ Merops - the peptidase database] {{Webarchive|url=https://web.archive.org/web/20061114180435/http://merops.sanger.ac.uk/ |date=2006-11-14 }}

{{Genomics-footer}}
{{Enzymes}}
{{Proteases}}
{{Cysteine proteases}}
{{Aspartic acid proteases}}
{{Portal bar|Biology|border=no}}

{{DEFAULTSORT:Proteolysis Map}}
[[Category:Protein databases]]
[[Category:Bioinformatics software]]
[[Category:Protein domains]]
[[Category:Protein families]]
[[Category:Peripheral membrane proteins]]
[[Category:EC 3.4|*]]
[[Category:EC 3.4.22|*]]
[[Category:Post-translational modification]]