title: MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
abstract: 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 hierarchical classifications 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 database has been expanded to include proteolytic enzymes other than peptidases. Special identifiers for peptidases from a variety of model organisms have been established so that orthologues can be detected in other species. A table of predicted active-site residue and metal ligand positions and the residue ranges of the peptidase domains in orthologues has been added to each peptidase summary. New displays of tertiary structures, which can be rotated or have the surfaces displayed, have been added to the structure pages. New indexes for gene names and peptidase substrates have been made available. Among the enhancements to existing features are the inclusion of small-molecule inhibitors in the tables of peptidase-inhibitor interactions, a table of known cleavage sites for each protein substrate, and tables showing the substrate-binding preferences of peptidases derived from combinatorial peptide substrate libraries.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. ndr@sanger.ac.uk
authors.forename: Neil D
authors.initials: ND
authors.lastname: Rawlings
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Barrett
authors.forename: Alex
authors.initials: A
authors.lastname: Bateman
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D030562:Databases, Protein; D006801:Humans; D008024:Ligands; D051379:Mice; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000145:classification*; D011480:Protease Inhibitors / Q000737:chemistry* / Q000145:classification*; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
chemical_list: D008024:Ligands; D011480:Protease Inhibitors; D010447:Peptide Hydrolases
references.citation: Biol Chem. 2007 Nov;388(11):1151-7
references.pmid: 17976007
references.citation: J Comput Aided Mol Des. 2002 Dec;16(12):871-81
references.pmid: 12825620
references.citation: Curr Med Chem. 2010;17(33):3968-95
references.pmid: 20939826
references.citation: Trends Biochem Sci. 1995 Sep;20(9):374
references.pmid: 7482707
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D392-401
references.pmid: 21036868
references.citation: Database (Oxford). 2009;2009:bap015
references.pmid: 20157488
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D249-54
references.pmid: 19854951
references.citation: Trends Biochem Sci. 1995 Nov;20(11):478-80
references.pmid: 8578593
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6
references.pmid: 18048412
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D227-33
references.pmid: 19892822
references.citation: Methods Enzymol. 1985;115:359-80
references.pmid: 3853075
references.citation: Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8
references.pmid: 3162770
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D320-5
references.pmid: 17991683
references.citation: PLoS Comput Biol. 2008 May 30;4(5):e1000069
references.pmid: 18516236
references.citation: Biochem J. 2004 Mar 15;378(Pt 3):705-16
references.pmid: 14705960
references.citation: J Biol Chem. 2011 Nov 4;286(44):38321-38328
references.pmid: 21832066
references.citation: Biochem J. 1993 Feb 15;290 ( Pt 1):205-18
references.pmid: 8439290
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):325-31
references.pmid: 9847218
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D160-4
references.pmid: 14681384
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51
references.pmid: 21097890