View source for The Proteolysis Map

[[Image:PMAP-logoV8-2blue.png|100px|thumb|right|'''PMAP logo''']]
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'''The Proteolysis MAP''' (PMAP) is an integrated web resource focused on [[proteases]]<ref>Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. PMAP: databases for analyzing proteolytic events and pathways. [[Nucleic Acids Research]]. 2008 Oct 8.[Epub ahead of print]</ref>. 

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

==History & 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]], Ph.D., 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. Funding: [[National Institutes of Health]] (RR020843, CA108959 [[GenBank]] , CA30199). Funding for open access charge: [[National Institutes of Health]] (RR020843, CA108959 [[GenBank]] , CA30199).

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

==The goal==
[[Proteolytic]] pathways, or [[proteolysis]], are the series of events controlled by [[proteases]] that occur in response to specific stimuli. In addition to the [[clotting]] of blood, the production of [[insulin]] can be viewed as a [[proteolytic]] pathway, as the activation, regulation and inhibition of that protein is the result of [[proteases]] reacting to changing [[glucose]] levels and triggering other [[proteases]] downstream.

==Database Content==
PMAP integrates five [[databases]] (DBs), linked together in one environment.
(1)ProteaseDB and (2)SubstrateDB, are driven by an automated annotation pipeline that generates dynamic ‘Molecule Pages’, rich in molecular information. (3)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 (4)ProfileDB is dedicated to information of the [[substrate]] recognition specificity of [[proteases]]. (5)PathwayDB, just begun accumulation of [[metabolic pathways]] whose function can be dynamically modeled in a rule-based manner.  Hypothetical [[networks]] are [[inferred]] by semi-automated culling of the literature. Additionally, [[protease]] [[software tools]] are available for the analysis of individual proteases and [[proteome]]-wide data sets.

==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.

==References==
<references />

==PMAP disambiguation==
The Proteolysis Map (PMAP) should NOT be confused with other [[acronyms]]:

'''Acronyms:'''
* [http://acronyms.thefreedictionary.com/PMAP List of eleven (11) different PMAP acronym and definitions]
	    
'''Individual protein names:'''
* PMAP (porcine myeloid antimicrobial peptides), such as [http://ca.expasy.org/uniprot/P49930 PMAP-23], [http://ca.expasy.org/uniprot/P49931 PMAP-36]; [http://ca.expasy.org/uniprot/P49932 PMAP-37] 

'''Management & organizations:'''
* [http://www.fda.gov/CDRH/ap-inspection/pmap-qa.html FDA Pilot Multi-Purpose Audit Program (PMAP)] 
* [http://hr.od.nih.gov/perfmgmt/form.htm Performance Management Appraisal Plan (PMAP) Form]
* [http://www.pmap.org Project Management Association of Professionals (PMAP)]
* [http://www.scbar.org/member_resources/practice_management_pmap Practice Management (PMAP)]
* [http://www.ucare.org/HEALTHPLANS/Pages/pmap.aspx The Prepaid Medical Assistance Program (PMAP)]
* 
'''Products:'''
* [http://www.alibaba.com/product-gs/208533292/Mono_Ammonium_Phosphate_Fertilizer_PMAP_.html Mono-Ammonium Phosphate Fertilizer (PMAP)]

'''UNIX/Linux/Basic commands:'''
* [http://compute.cnr.berkeley.edu/cgi-bin/man-cgi?pmap+1 User Commands pmap(1)]
* [http://linux.die.net/man/1/pmap pmap - report memory map of a process]
* [http://wolfpackempire.com/infopages/pmap.html Basic Command : PMAP]

'''SUN port mapper:'''
* [http://www.protocols.com/pbook/sunfamily.htm#PMAP The Port Mapper (PMAP) protocol]

==External links==
* [http://www.proteolysis.org/ Official website]
* [http://www.burnham.org/ Host institution website]
* [http://cutdb.burnham.org/ Proteolysis Cut Site database - curated expert annotation from users]
* [http://substrate.burnham.org/ Protease cut sites graphical interface]
* [http://www.expasy.org/tools/peptidecutter/ Protease cutting predictor]
* [http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html List of proteases and their specificities]
* [http://www.protease.org/ International Proteolysis Society]
* [http://merops.sanger.ac.uk/ Merops - the peptidase database]
* [http://www.sciencegateway.org/resources/protease.htm List of protease inhibitors]
* {{MeshName|Proteases}}

==See also==

* [[Proteolysis]]
* [[Protease]]
* [[Metabolic pathway]]
* [[Cytoscape]]
* [[Computational genomics]]
* [[Metabolic network modelling]]
* [[Protein-protein interaction prediction]]
* [[Autophagy network]]
* [[SUMO network]]

{{Enzymes}}
{{Proteases}}
{{Cysteine proteases}}
{{Aspartic acid proteases}}
{{SIB}}
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[[Category:EC 3.4|*]]
[[Category:Posttranslational modification]]
[[Category:EC 3.4.22]]
[[Category:Programmed cell death]]
[[Category:Apoptosis]]
[[Category:Molecular biology]]
[[Category:Bioinformatics databases]]
[[Category:Bioinformatics software]]
[[Category:Systems biology]]
[[Category:Mathematical biology]]
[[Category:Protein domains]]
[[Category:Protein families]]
[[Category:Peripheral membrane proteins]]

[[ca:Peptidasa]]
[[cs:Proteázy]]
[[da:Protease]]
[[de:Peptidase]]
[[el:Πεπτιδάση]]
[[es:Peptidasa]]
[[fr:Peptidase]]
[[it:Proteasi]]
[[he:פרוטאז]]
[[hu:Proteáz]]
[[nl:Protease]]
[[ja:プロテアーゼ]]
[[no:Protease]]
[[oc:Proteasa]]
[[pl:Proteazy]]
[[pt:Protease]]
[[ru:Протеаза]]
[[simple:Protease]]
[[sl:Peptidaza]]
[[sv:Proteas]]
[[tr:Proteaz]]
[[uk:Протеаза]]
[[zh:蛋白酶]]
[[de:Caspasen]]
[[es:Caspasa]]
[[fr:Caspase]]
[[it:Caspasi]]
[[nl:Caspase]]
[[ja:カスパーゼ]]
[[pl:Kaspazy]]
[[pt:Caspase]]
[[sv:Caspaser]]
[[de:Aspartatproteasen]]

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