Skip Navigation



Nucleic Acids Research Advance Access published online on October 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn683
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (10587K) Freely available
Right arrow Screen PDF (1116K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/suppl_1/D611    most recent
gkn683v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Igarashi, Y.
Right arrow Articles by Eroshkin, A. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Igarashi, Y.
Right arrow Articles by Eroshkin, A. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
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.

Database Issue

PMAP: databases for analyzing proteolytic events and pathways

Yoshinobu Igarashi1, Emily Heureux1, Kutbuddin S. Doctor1, Priti Talwar1, Svetlana Gramatikova1, Kosi Gramatikoff1, Ying Zhang1, Michael Blinov3, Salmaz S. Ibragimova2, Sarah Boyd4, Boris Ratnikov1, Piotr Cieplak1, Adam Godzik1, Jeffrey W. Smith1, Andrei L. Osterman1 and Alexey M. Eroshkin1,*

1The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center at The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA, 2Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 10, Novosibirsk 630090, Russia, 3Center of Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA and 4Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia

*To whom correspondence should be addressed. Tel: +1 858 646 3100/3923; Fax: +1 858 713 9949; Email: eroshkin{at}burnham.org

Received August 15, 2008. Revised September 19, 2008. Accepted September 23, 2008.

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.