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Nucleic Acids Research Advance Access published online on November 16, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl813
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© 2006 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

CutDB: a proteolytic event database

Yoshinobu Igarashi, Alexey Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei L. Osterman and Adam Godzik*

Burnham Institute for Medical Research, 10901 North Torrey Pines Road La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Tel: +1 858 646 3168; Fax: +1 858 713 9949; Email: adam{at}burnham.org

Received August 15, 2006. Revised October 2, 2006. Accepted October 3, 2006.

Beyond the well-known role of proteolytic machinery in protein degradation and turnover, many specialized proteases play a key role in various regulatory processes. Thousands of highly specific proteolytic events are associated with normal and pathological conditions, including bacterial and viral infections. However, the information about individual proteolytic events is dispersed over multiple publications and is not easily available for large-scale analysis. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content. CutDB is publicly available at http://cutdb.burnham.org.


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