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
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    • "Unfortunately, the MEROPS database often does not include the current proteomic data because it depends on the good will of the researchers to provide their results. Other degradomic databases, including CutDB [94], TopFIND [95e97] and TOPPR [98], were created by different research groups; however, they are often specific to a particular methodology, which limits their general applicability and the availability of the data for further processing (different groups use different proteomic pipelines and data processing software). We believe that the true future challenge will be integration of all available degradomic data, which would enable data mining and the determination of common rules and denominators of proteolytic processes. "
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    ABSTRACT: Proteolytic cleavage is a ubiquitous, irreversible, posttranslational modification that changes protein structure and function and plays an important role in numerous physiological and pathological processes. Over the last decade, proteases have become increasingly important clinical targets because many of their inhibitors are already used in the clinic or in various stages of clinical testing. Therefore, a better understanding of protease action and their repertoires of physiological substrates can not only provide an important insight into their mechanisms of action but also open a path toward novel drug design. Historically, proteases and their substrates were mainly studied on a case-by-case basis, but recent advancements in mass spectrometry-based proteomics have enabled proteolysis studies on a global scale. Because there are many different types of proteases that can operate in various cellular contexts, multiple experimental approaches for their degradomic characterization had to be developed. The present paper reviews the mass spectrometry-based approaches for determining the proteolytic events in complex biological samples. The methodologies for substrate identification and the determination of protease specificity are discussed, with a special focus on terminomic strategies, which combine peptide labeling and enrichment.
    Full-text · Article · Oct 2015 · Biochimie
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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. "

    Full-text · Dataset · Sep 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. "
    Dataset: Klein 2013a

    Full-text · Dataset · Sep 2015
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