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CutDB: a proteolytic event database

Y. Igarashi, A. Eroshkin, S. Gramatikova, K. Gramatikoff, Y. Zhang, J. W. Smith, A. L. Osterman, A. Godzik
2007 Nucleic Acids Research  
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.  ...  Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications.  ...  Alex Bateman and Ms Olivia Haggis for their suggestions and sending us their proteolytic event data.  ... 
doi:10.1093/nar/gkl813 pmid:17142225 pmcid:PMC1669773 fatcat:gtphaww4ffcvdjj2aj3lzlnzda

PMAP: databases for analyzing proteolytic events and pathways

Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak (+4 others)
2008 Nucleic Acids Research  
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  ...  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.  ...  CutDB CutDB is a database of individual proteolytic events (cleavage sites) culled from the literature.  ... 
doi:10.1093/nar/gkn683 pmid:18842634 pmcid:PMC2686432 fatcat:kp24qbe6vjhmfdsqvhhswibbcu

Sequence-derived structural features driving proteolytic processing

Alexander A. Belushkin, Dmitry V. Vinogradov, Mikhail S. Gelfand, Andrei L. Osterman, Piotr Cieplak, Marat D. Kazanov
2013 Proteomics  
captured in CutDB.  ...  Here, we analyzed the relative importance in proteolysis of various structural features derived from substrate sequences using a dataset of more than five thousand experimentally verified proteolytic events  ...  CutDB is a part of the PMAP web-environment that integrates five databases reflecting different aspects of proteolysis, such as proteolytic events, pathways, enzymes, substrates, and profiles.  ... 
doi:10.1002/pmic.201300416 pmid:24227478 pmcid:PMC3926948 fatcat:hambphxqk5hsjheaeewmajwkre

CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

Sonu Kumar, Boris I. Ratnikov, Marat D. Kazanov, Jeffrey W. Smith, Piotr Cieplak, Effie C Tsilibary
2015 PLoS ONE  
However, recent statistical analysis of CutDB, the proteolytic event database [3], demonstrated that proteolytic events were uniformly distributed among three types of secondary structures, although with  ...  It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events.  ...  In summary, the CleavPredict is a useful platform for reasoning about proteolytic events.  ... 
doi:10.1371/journal.pone.0127877 pmid:25996941 pmcid:PMC4440711 fatcat:qnztpllphrdvvbtg476vfq2z3e

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events

Niklaas Colaert, Davy Maddelein, Francis Impens, Petra Van Damme, Kim Plasman, Kenny Helsens, Niels Hulstaert, Joël Vandekerckhove, Kris Gevaert, Lennart Martens
2012 Nucleic Acids Research  
These cleavage events were identified with COmbinded FRActional DIagonal Chromatography proteomics technologies, and the resulting database is provided with full data provenance.  ...  We here present The Online Protein Processing Resource (TOPPR; http://iomics.ugent.be/toppr/), an online database that contains thousands of published proteolytically processed sites in human and mouse  ...  A number of databases are currently available that disseminate protein processing events.  ... 
doi:10.1093/nar/gks998 pmid:23093603 pmcid:PMC3531153 fatcat:ozhqolemgzccpov6zfs6x2njlm

Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry

Nitin Gupta, Kim K. Hixson, David E. Culley, Richard D. Smith, Pavel A. Pevzner
2010 Proteomics  
Finally, we show that comparative analysis of multiple proteases can be used to detect putative in vivo proteolytic sites on a proteome-wide scale.  ...  In this study, we describe MS-Proteolysis, a software tool for identifying putative sites of in vivo proteolytic cleavage using label-free mass spectrometry.  ...  Since little is known about regulatory proteolysis in Shewanella apart from NME and signal peptides (CutDB database [38] does not report any proteolytic events in Shewanella), it remains to be verified  ... 
doi:10.1002/pmic.200900821 pmid:20597098 pmcid:PMC3220954 fatcat:yhtjl7x625dfzaiotdnh5iwjca

Identification of the novel substrates for caspase-6 in apoptosis using proteomic approaches

Jin Hwa Cho, Phil Young Lee, Woo-Chan Son, Seung-Wook Chi, Byoung Chul Park, Jeong-Hoon Kim, Sung Goo Park
2013 BMB Reports  
It is typically accompanied by the activation of a class of cysteine proteases called caspases.  ...  Apoptosis, programmed cell death, is a process involved in the development and maintenance of cell homeostasis in multicellular organisms.  ...  To determine whether the identified candidates were novel or not, we carried out a database search at The CASBAH (http://bioinf.gen.tcd.ie/casbah) and the CutDB, a proteolytic event database (http://cutdb.burnham.org  ... 
doi:10.5483/bmbrep.2013.46.12.081 pmid:24195789 pmcid:PMC4133863 fatcat:jjjp7h3eajatfmxkmlskt5g2hu

Targeted degradomics in protein terminomics and protease substrate discovery

Simonas Savickas, Ulrich auf dem Keller
2017 Biological chemistry  
AbstractTargeted degradomics integrates positional information into mass spectrometry (MS)-based targeted proteomics workflows and thereby enables analysis of proteolytic cleavage events with unprecedented  ...  Werner (ETH Zurich, Switzerland) for her continuous support of our work and the Swiss National Science Foundation for funding with help of a project grant (31003A_163216).  ...  Targeted degradomics workflows start with identifying the proteolytic cleavage of interest in protease cleavage databases like CutDB, MEROPS or UniProt.  ... 
doi:10.1515/hsz-2017-0187 pmid:28850541 fatcat:nepawuma6recjbfvn3amh2tuqy

Structural Determinants of Limited Proteolysis

Marat D. Kazanov, Yoshinobu Igarashi, Alexey M. Eroshkin, Piotr Cieplak, Boris Ratnikov, Ying Zhang, Zhanwen Li, Adam Godzik, Andrei L. Osterman, Jeffrey W. Smith
2011 Journal of Proteome Research  
The analysis was performed on a dataset of >200 proteolytic events documented in CutDB for a variety of mammalian regulatory proteases and their physiological substrates with known 3D structures.  ...  A better understanding of mechanisms that control this process is required for discovering new proteolytic events and for developing inhibitors with potential therapeutic value.  ...  This work was supported by NIH grant number RR020843, "Center on Proteolytic Pathways" (to JWS).  ... 
doi:10.1021/pr200271w pmid:21682278 pmcid:PMC3164237 fatcat:4s7ge7zzgjdotkhx4zzfbyf6b4

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz, Iwaniak, Darewicz
2019 International Journal of Molecular Sciences  
The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents  ...  The database is continuously updated and modified.  ...  A proteolytic event is understood as a case of cleavage of an individual peptide bond. This term has been introduced in the CutDB database [56] .  ... 
doi:10.3390/ijms20235978 pmid:31783634 pmcid:PMC6928608 fatcat:kllch44xkvbp5fizp2qaklfg3m

Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology

Lindsay D. Rogers, Christopher M. Overall
2013 Molecular & Cellular Proteomics  
events.  ...  Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease.  ...  and inhibitors (71) CutDB Annotation of individual proteolytic events, both actual and predicted 11,081 proteolytic events from 601 proteases and 3387 substrates This paper is available  ... 
doi:10.1074/mcp.m113.031310 pmid:23887885 pmcid:PMC3861706 fatcat:wp4o5og5bnecxpxawdp2tveqa4

The Degradome database: expanding roles of mammalian proteases in life and disease

José G. Pérez-Silva, Yaiza Español, Gloria Velasco, Víctor Quesada
2015 Nucleic Acids Research  
Since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology  ...  The Degradome database can be accessed through its web interface at http://degradome.uniovi.es.  ...  For instance, CutDB documents actual and predicted proteolytic events, but does not provide a global view of the proteases themselves (15) .  ... 
doi:10.1093/nar/gkv1201 pmid:26553809 pmcid:PMC4702854 fatcat:4imogxun3neh5ezykumnc2jdcy

A large and accurate collection of peptidase cleavages in the MEROPS database

N. D. Rawlings
2009 Database: The Journal of Biological Databases and Curation  
Database URL: http://merops.sanger.ac.uk .  ...  The MEROPS database is an Internet resource containing information on peptidases, their substrates and inhibitors.  ...  Because the CutDB database includes only cleavages thought to be of physiological relevance and those that can be included in their proteolytic pathways, it has fewer cleavages than in the MEROPS collection  ... 
doi:10.1093/database/bap015 pmid:20157488 pmcid:PMC2790309 fatcat:6l5q7bndvzakbahx7uzckmo32e

Combinatorial degradomics: Precision tools to unveil proteolytic processes in biological systems

Simonas Savickas, Philipp Kastl, Ulrich auf dem Keller
2020 Biochimica et Biophysica Acta - Proteins and Proteomics  
Proteolytic processing is an irreversible PTM generating novel isoforms of a mature protein termed proteoforms.  ...  Here, we give an overview of currently available MS-based degradomics methods and outline how they can be optimally applied to study protease cleavage events.  ...  Data obtained by discovery degradomics approaches is stored in databases like MEROPS (https://www.ebi.ac.uk/merops/), CutDB (https://omictools.com/cutdb-tool), TopFIND (http://clipserve.clip.ubc.ca/topfind  ... 
doi:10.1016/j.bbapap.2020.140392 pmid:32087360 fatcat:jkfuzriw4jh3jc6jkreudak7tm

Human Protein Reference Database--2009 update

T. S. Keshava Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, A. Venugopal, L. Balakrishnan, A. Marimuthu (+18 others)
2009 Nucleic Acids Research  
Human Protein Reference Database (HPRD-http:// www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins.  ...  We have recently added a number of new features in HPRD.  ...  ACKNOWLEDGEMENTS We thank all investigators and 'Molecule Authorities' who have provided valuable feedback about individual entries in this database.  ... 
doi:10.1093/nar/gkn892 pmid:18988627 pmcid:PMC2686490 fatcat:x3anufiurnh3bltpprkxbk3tom
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