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MEROPS: the peptidase database.

Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ - Nucleic Acids Res. (2007)

Bottom Line: Peptidases (proteolytic enzymes or proteases), their substrates and inhibitors are of great relevance to biology, medicine and biotechnology.Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays to show peptidase specificity compiled from our collection of known substrate cleavages; tables of peptidase-inhibitor interactions; and dynamically generated alignments of representatives of each protein species at the family level.New ways to compare peptidase and inhibitor complements between any two organisms whose genomes have been completely sequenced, or between different strains or subspecies of the same organism, have been devised.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ndr@sanger.ac.uk

ABSTRACT
Peptidases (proteolytic enzymes or proteases), 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 organizational principle of the database is a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families and in turn grouped into clans. Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays to show peptidase specificity compiled from our collection of known substrate cleavages; tables of peptidase-inhibitor interactions; and dynamically generated alignments of representatives of each protein species at the family level. New ways to compare peptidase and inhibitor complements between any two organisms whose genomes have been completely sequenced, or between different strains or subspecies of the same organism, have been devised.

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Example SMI page. The summary page for the inhibitor pepstatin is shown.
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Figure 2: Example SMI page. The summary page for the inhibitor pepstatin is shown.

Mentions: The MEROPS database has included protein inhibitors of peptidases since 2004. However, there are many other inhibitors that are not proteins, including peptides and synthetic inhibitors, which we term small molecule inhibitors (SMIs). These include many that are laboratory reagents used in the characterization of peptidases, and others that are drugs such as the inhibitors of the retropepsin of the HIV virus. Information about SMIs has now been collated and is presented within MEROPS. There is no satisfactory, single method to classify SMIs, so their names and alternative names are simply listed alphabetically. For many SMIs summaries have been written. Each summary contains a recommended name, other names including the chemical name, history, details of peptidases inhibited, a description of the mechanism of inhibition, an image of the chemical structure, a cross reference to the PubChem database (9), comments and recommended reviews. An example summary page for pepstatin is shown in Figure 2. In addition, a ‘Relevant Inhibitors’ field has been added to the peptidase summaries, which lists SMIs that are known to inhibit the peptidase or that do not inhibit even if expected to. Each item in the list has a link to the relevant SMI summary.Figure 2.


MEROPS: the peptidase database.

Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ - Nucleic Acids Res. (2007)

Example SMI page. The summary page for the inhibitor pepstatin is shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238837&req=5

Figure 2: Example SMI page. The summary page for the inhibitor pepstatin is shown.
Mentions: The MEROPS database has included protein inhibitors of peptidases since 2004. However, there are many other inhibitors that are not proteins, including peptides and synthetic inhibitors, which we term small molecule inhibitors (SMIs). These include many that are laboratory reagents used in the characterization of peptidases, and others that are drugs such as the inhibitors of the retropepsin of the HIV virus. Information about SMIs has now been collated and is presented within MEROPS. There is no satisfactory, single method to classify SMIs, so their names and alternative names are simply listed alphabetically. For many SMIs summaries have been written. Each summary contains a recommended name, other names including the chemical name, history, details of peptidases inhibited, a description of the mechanism of inhibition, an image of the chemical structure, a cross reference to the PubChem database (9), comments and recommended reviews. An example summary page for pepstatin is shown in Figure 2. In addition, a ‘Relevant Inhibitors’ field has been added to the peptidase summaries, which lists SMIs that are known to inhibit the peptidase or that do not inhibit even if expected to. Each item in the list has a link to the relevant SMI summary.Figure 2.

Bottom Line: Peptidases (proteolytic enzymes or proteases), their substrates and inhibitors are of great relevance to biology, medicine and biotechnology.Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays to show peptidase specificity compiled from our collection of known substrate cleavages; tables of peptidase-inhibitor interactions; and dynamically generated alignments of representatives of each protein species at the family level.New ways to compare peptidase and inhibitor complements between any two organisms whose genomes have been completely sequenced, or between different strains or subspecies of the same organism, have been devised.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ndr@sanger.ac.uk

ABSTRACT
Peptidases (proteolytic enzymes or proteases), 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 organizational principle of the database is a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families and in turn grouped into clans. Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays to show peptidase specificity compiled from our collection of known substrate cleavages; tables of peptidase-inhibitor interactions; and dynamically generated alignments of representatives of each protein species at the family level. New ways to compare peptidase and inhibitor complements between any two organisms whose genomes have been completely sequenced, or between different strains or subspecies of the same organism, have been devised.

Show MeSH