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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 Substrate...

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Autores principales: Igarashi, Yoshinobu, Heureux, Emily, Doctor, Kutbuddin S., Talwar, Priti, Gramatikova, Svetlana, Gramatikoff, Kosi, Zhang, Ying, Blinov, Michael, Ibragimova, Salmaz S., Boyd, Sarah, Ratnikov, Boris, Cieplak, Piotr, Godzik, Adam, Smith, Jeffrey W., Osterman, Andrei L., Eroshkin, Alexey M.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686432/
https://www.ncbi.nlm.nih.gov/pubmed/18842634
http://dx.doi.org/10.1093/nar/gkn683
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author Igarashi, Yoshinobu
Heureux, Emily
Doctor, Kutbuddin S.
Talwar, Priti
Gramatikova, Svetlana
Gramatikoff, Kosi
Zhang, Ying
Blinov, Michael
Ibragimova, Salmaz S.
Boyd, Sarah
Ratnikov, Boris
Cieplak, Piotr
Godzik, Adam
Smith, Jeffrey W.
Osterman, Andrei L.
Eroshkin, Alexey M.
author_facet Igarashi, Yoshinobu
Heureux, Emily
Doctor, Kutbuddin S.
Talwar, Priti
Gramatikova, Svetlana
Gramatikoff, Kosi
Zhang, Ying
Blinov, Michael
Ibragimova, Salmaz S.
Boyd, Sarah
Ratnikov, Boris
Cieplak, Piotr
Godzik, Adam
Smith, Jeffrey W.
Osterman, Andrei L.
Eroshkin, Alexey M.
author_sort Igarashi, Yoshinobu
collection PubMed
description 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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spelling pubmed-26864322009-06-15 PMAP: databases for analyzing proteolytic events and pathways Igarashi, Yoshinobu Heureux, Emily Doctor, Kutbuddin S. Talwar, Priti Gramatikova, Svetlana Gramatikoff, Kosi Zhang, Ying Blinov, Michael Ibragimova, Salmaz S. Boyd, Sarah Ratnikov, Boris Cieplak, Piotr Godzik, Adam Smith, Jeffrey W. Osterman, Andrei L. Eroshkin, Alexey M. Nucleic Acids Res Articles 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. Oxford University Press 2009-01 2008-10-08 /pmc/articles/PMC2686432/ /pubmed/18842634 http://dx.doi.org/10.1093/nar/gkn683 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Igarashi, Yoshinobu
Heureux, Emily
Doctor, Kutbuddin S.
Talwar, Priti
Gramatikova, Svetlana
Gramatikoff, Kosi
Zhang, Ying
Blinov, Michael
Ibragimova, Salmaz S.
Boyd, Sarah
Ratnikov, Boris
Cieplak, Piotr
Godzik, Adam
Smith, Jeffrey W.
Osterman, Andrei L.
Eroshkin, Alexey M.
PMAP: databases for analyzing proteolytic events and pathways
title PMAP: databases for analyzing proteolytic events and pathways
title_full PMAP: databases for analyzing proteolytic events and pathways
title_fullStr PMAP: databases for analyzing proteolytic events and pathways
title_full_unstemmed PMAP: databases for analyzing proteolytic events and pathways
title_short PMAP: databases for analyzing proteolytic events and pathways
title_sort pmap: databases for analyzing proteolytic events and pathways
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686432/
https://www.ncbi.nlm.nih.gov/pubmed/18842634
http://dx.doi.org/10.1093/nar/gkn683
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