MEROPS

For other uses, see Merops.
MEROPS
Content
Description MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Contact
Research center The Wellcome Trust Sanger Institute
Authors Neil D Rawlings
Primary citation Rawlings & al. (2012)[1]
Release date 2010
Access
Website http://merops.sanger.ac.uk

MEROPS is an on-line database for peptidases (also known as proteases) and their inhibitors.[2] The classification scheme for peptidases was published by Rawlings & Barrett in 1993,[3] and that for protein inhibitors by Rawlings et al. in 2004.[4]

Overview

The classification is based on similarities at the tertiary and primary structural levels. Comparisons are restricted to that part of the sequence directly involved in the reaction, which in the case of a peptidase must include the active site, and for a protein inhibitor the reactive site. The classification is hierarchical: sequences are assembled into families, and families are assembled into clans. A family is assembled around a type example, the sequence of a well-characterized peptidase or inhibitor. All other sequences in the family must be related to the family type example, either directly or through a transitive relationship involving one or more sequences already shown to be family members. Typically, FastA or BlastP are used to establish sequence relationships, with an expect value of 0.001 or lower taken to be statistically significant. A clan is also assembled around a type example, this being the structure of a well-characterized peptidase or inhibitor. A family is included in a clan if the tertiary structure of a family member can be shown to be related to that of the clan type example. Typically, DALI is used to establish clan membership, with a z score of 6.00 standard deviation units or above considered to be statistically significant. For peptidases, other evidence to indicate that families are related when a tertiary structure is absent includes the same order of catalytic residues in the sequences.

See also

References

  1. ↑ Rawlings, Neil D; Barrett Alan J; Bateman Alex (Jan 2012). "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors". Nucleic Acids Res. England. 40 (Database issue): D343–50. doi:10.1093/nar/gkr987. PMC 3245014Freely accessible. PMID 22086950.
  2. ↑ Rawlings ND, Barrett AJ, Bateman A (January 2010). "MEROPS: the peptidase database". Nucleic Acids Res. 38 (Database issue): D227–33. doi:10.1093/nar/gkp971. PMC 2808883Freely accessible. PMID 19892822.
  3. ↑ Rawlings, N.D. & Barrett, A.J. (1993) Evolutionary families of peptidases. Biochem J 290, 205-218.
  4. ↑ Rawlings, N.D., Tolle, D.P. & Barrett, A.J. (2004) Evolutionary families of peptidase inhibitors. Biochem J 378, 705-716.
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