MEROPS: the peptidase database

By Neil D. Rawlings, Alan J. Barrett, Alex Bateman. Nucleic Acids Res., 2009

1,954 citations recorded by the source corpus.

Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The classification framework is used for attaching information at each level. An important focus of the database has become distinguishing one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact. We have collected over 39 000 known cleavage sites in proteins, peptides and synthetic substrates. These allow us to display peptidase specificity and alignments of protein substrates to give an indication of how well a cleavage site is conserved, and thus its probable physiological relevance. While the number of new peptidase families and clans has only grown slowly the number of complete genomes has greatly increased. This has allowed us to add an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species.

Subfields: Biotechnology, Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/677872c4051ee37a13161ecb8efa32fcbadc7a80

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Citations in the corpus

Native and Biotechnologically Engineered Plant Proteases with Industrial Applications (2011, background): “Majority of plant APs, together with pepsin-like enzymes from many different origins, belong to the A1 family (Rawlings et al. 2010).”
Extracellular matrix structure. (2016, neutral): “L, K, O, S, V, X and W (cysteine proteases) [273].”
Protein sectors: evolutionary units of three-dimensional structure (2009, methodology): “Here, we carry out this analysis using a classic model system for enzyme catalysis, the S1A family of serine proteases (Hedstrom, 2002; Rawlings and Barrett, 1994; Rawlings et al., 2008).”
Enhanced methyltransferase activity of SMYD3 by the cleavage of its N-terminal region in human cancer cells (2008, background): “A public peptidase database termed ‘MEROPS’ (Rawlings et al., 2006) predicted Caspase-3, -7 and -8 as candidate proteases for the cleavage of ‘SDPL’, the amino acid sequence between codons 33 and 36 in SMYD3.”
Biochemistry and molecular biology of gelatinase B or matrix metalloproteinase-9 (MMP-9): The next decade (2013, background): “in Clan MA of proteolytic enzymes (Barrett et al., 2012; Rawlings et al., 2010).”
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors (2015, background): “Similarly, a collection of peptidase-inhibitor interactions has also been established, which provides evidence for distinguishing peptidases and inhibitors (6).”
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 (2010, neutral): “0 focuses on two protein superfamilies including protein products commonly encoded by LTR retroelements and their host genomes; the chromodomain superfamily (11) and clan AA of aspartic peptidases (12,13).”
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors (2013, background): “In the 2 years since the previous article (14), despite the number of sequences in the database having increasing by over a third, only 18 new families and 4 new clans have been added.”
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database (2017, background): “Similarly, a collection of peptidase-inhibitor interactions has also been established, which provides evidence for distinguishing peptidases and inhibitors (6).”
Cleavage Entropy as Quantitative Measure of Protease Specificity (2013, methodology): “were extracted from the MEROPS database [31].”