Nucleic Acids Research, Vol 27, Issue 1 325-331, Copyright © 1999 by Oxford University Press
ND Rawlings and AJ Barrett
The MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/Merops.+ ++htm)
provides a catalogue and structure-based classification of peptidases (i.e.
all proteolytic enzymes). This is a large group of proteins (approximately
2% of all gene products) that is of particular importance in medicine and
biotechnology. An index of the peptidases by name or synonym gives access
to a set of files termed PepCards each of which provides information on a
single peptidase. Each card file contains information on classification and
nomenclature, and hypertext links to the relevant entries in online
databases for human genetics, protein and nucleic acid sequence data and
tertiary structure. Another index provides access to the PepCards by
organism name so that the user can retrieve all known peptidases from a
particular species. The peptidases are classified into families on the
basis of statistically significant similarities between the protein
sequences in the part termed the 'peptidase unit' that is most directly
responsible for activity. Families that are thought to have common
evolutionary origins and are known or expected to have similar tertiary
folds are grouped into clans. The MEROPS database provides sets of files
called FamCards and ClanCards describing the individual families and clans.
Each FamCard document provides links to other databases for sequence motifs
and secondary and tertiary structures, and shows the distribution of the
family across the major kingdoms of living creatures. Release 3.03 of
MEROPS contains 758 peptidases, 153 families and 22 clans. We suggest that
the MEROPS database provides a model for a way in which a system of
classification for a functional group of proteins can be developed and used
as an organizational framework around which to assemble a variety of
related information.
ARTICLES
MEROPS: the peptidase database
MRC Molecular Enzymology Laboratory, The Babraham Institute, Babraham, Cambridgeshire CB2 4AT, UK. neil.rawlings@bbsrc.ac.uk
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