Article

CutDB: a proteolytic event database

Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2007; 35(Database issue):D546-9. DOI: 10.1093/nar/gkl813
Source: PubMed

ABSTRACT 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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Available from: Alexey M Eroshkin, Jul 23, 2015
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    • "The main component of Proteasix is the underlying cleavage site database (CS database). The CS database has been built using information on human proteases from CutDB [13], Uniprot and the literature, collected through both manual literature mining and automated Java scripts. Each protease was associated with their corresponding CS sequences in their longest form (i.e. "
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    • "MMPs in primary explant collective cell migration T. M. McDonald et al. site comparisons were performed using CutDB (Igarashi et al., 2007) to identify cleavage sites in pro-MMPs and conservation between human and zebrafish sites determined using the alignments generated by BLAST. "
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