Welcome to the MEROPS blog. This is a forum to announce new releases of the MEROPS databases and to get feedback from our users for matters concerning the classification and nomenclature of peptidases, their substrates and inhibitors.
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MEROPS Blog 
August 12, 2009 at 5:21 pm
Dear MEROPS Members,
I like your Peptide database very much.
But how can I solve following problem:
I have a aminoacid sequence of about 100 amino acids in length. I kow that a zinc-dependent protease, most likely a matrix metalloproteinase will cleave that peptide. The cleavage site is unknown in a range of 30 amino acids. Which of the 23 MMPs will cleave is also unknown. To learn more about the cleavage sites of each MMP within the peptide, a “window” to fill in the amino acid sequence in one letter code and a prediction outcome for cleavage sites of certain proteases, especially the 23 matrix metalloproteinases will very helpful for my research. Please, can you help me to solve this problem?
With best regards
Wolfgang
August 26, 2009 at 9:52 am
The problem of trying to predict cleavage positions in native proteins is very complex. Not only does it require a very full knowledge of peptidase specificity, but it also requires an understanding of the tertiary fold of the substrate to know which bonds might be accessible and which are buried. Most specificity studies are done on denatured proteins or on peptides with little structure, just to remove the complexity that folding brings to the problem. Even so, of the 2000+ different peptidases, we have only 300 peptidases with ten or more substrates, and I recently calculated that around 400 cleavages in substrates are required to map a peptidase’s specificity accurately. There are less than a dozen peptidases that have been so well studied.
So the chances of us devising the tools you would like to see are a long way off, simply because there isn’t enough data.
August 27, 2011 at 8:20 pm
What is the abbreviation MEROPS short for?
June 10, 2013 at 2:53 pm
MEROPS is not an abbreviation but Greek for the bee-eater. To understand why the database is named after the bird, please look at the following documentation: http://merops.sanger.ac.uk/about/history.shtml#BEGINNING.