The Proteolysis Map: Difference between revisions
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[[Image:PMAP-logoV8-2blue.png|100px|thumb|right|'''PMAP logo''']] | [[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>. | '''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>. | ||
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==History & Funding== | ==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 | 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== | ==Focal point== | ||
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==Database Content== | ==Database Content== | ||
PMAP integrates five [[databases]] (DBs), linked together in one environment. | 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 | (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== | ==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 | 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== | ||
{{reflist|2}} | |||
==PMAP disambiguation== | ==PMAP disambiguation== | ||
The Proteolysis Map (PMAP) should NOT be confused with other | The Proteolysis Map (PMAP) should NOT be confused with other acronyms: | ||
'''Acronyms:''' | '''Acronyms:''' | ||
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{{Cysteine proteases}} | {{Cysteine proteases}} | ||
{{Aspartic acid proteases}} | {{Aspartic acid proteases}} | ||
{{genomics-footer}} | {{genomics-footer}} | ||
Latest revision as of 15:29, 6 September 2012
The Proteolysis MAP (PMAP) is an integrated web resource focused on proteases[1].
Rationale
PMAP is to aid the protease researchers in reasoning about proteolytic 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[2] 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
- ↑ 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]
- ↑ 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
PMAP disambiguation
The Proteolysis Map (PMAP) should NOT be confused with other acronyms:
Acronyms:
Individual protein names:
Management & organizations:
- FDA Pilot Multi-Purpose Audit Program (PMAP)
- Performance Management Appraisal Plan (PMAP) Form
- Project Management Association of Professionals (PMAP)
- Practice Management (PMAP)
- The Prepaid Medical Assistance Program (PMAP)
Products:
UNIX/Linux/Basic commands:
SUN port mapper:
External links
- Official website
- Host institution website
- Proteolysis Cut Site database - curated expert annotation from users
- Protease cut sites graphical interface
- Protease cutting predictor
- List of proteases and their specificities
- International Proteolysis Society
- Merops - the peptidase database
- List of protease inhibitors
- Proteases at the US National Library of Medicine Medical Subject Headings (MeSH)
See also
- Proteolysis
- Protease
- Metabolic pathway
- Cytoscape
- Computational genomics
- Metabolic network modelling
- Protein-protein interaction prediction
- Autophagy network
- SUMO network
ca:Peptidasa cs:Proteázy da:Protease de:Peptidase el:Πεπτιδάση it:Proteasi he:פרוטאז hu:Proteáz nl:Protease no:Protease oc:Proteasa simple:Protease sl:Peptidaza sv:Proteas uk:Протеаза de:Caspasen it:Caspasi nl:Caspase sv:Caspaser de:Aspartatproteasen