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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...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2009
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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. |
format | Text |
id | pubmed-2686432 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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