Archive for April, 2009

Bug fixes

April 15, 2009

The following bugs have been fixed:

  • Substrate alignment display: highlighting of conserved and preferred residues has been corrected for the unusual situation where the sequence of the protein with known cleavages started at position 1 in the alignment; i.e. there were no other sequences with N-terminal extentions.  Previously highlighting had been one residue out.
  • Specificity heatmap: the shades of green in this display have been altered.  Previously highlighting for residues occurring in more than 40% of cleavages but less than 50% for a particular position (P4 to P4′) was too dark and indistinguishable from the black background indicating no preference.
  • Peptidase distribution display: the bug that was preventing several tree tip labels from being highlighted has been fixed. 
Advertisements

MEROPS 8.4

April 15, 2009

MEROPS 8.4 was released on 3 April 2009. New features include the following:

Substrate indexes
Two indexes for peptidase substrates have been added. These are accessible from the left-hand green menu. The first index shows the count of known substrate cleavages per peptidase, ordered by and linked to the MEROPS identifier. Three counts are shown: the total number in the MEROPS collection, the total number of physiological substrates (peptides and proteins) and the total number of non-physiological substrates (peptides and synthetic substrates). The second index is ordered by substrate name and shows the MEROPS identifier of the peptidases known to cleave each substrate and the total number of cleavages performed by each peptidase. For substrates than can be mapped to the UniProt protein sequence database the UniProt identifier is shown with a link to the MEROPS utility which shows all cleavages of this protein in the MEROPS collection.

Substrate pages
We have introduced “flags” on the substrate pages to indicate the method used to identify the cleavage position. The flags are as follows: NT shows that the cleavage position was determined by N-Terminal sequencing, MS shows that the peptide composition was determined by mass-spectroscopy (MS) and the cleavage position computed, MU shows that the cleavage position was determined by site-directed MUtagenesis, CS indicates that the cleavage position was postulated from a concensus motif (CS) within the protein sequence.

Release of signal and transit peptides and initiating methionine
Cleavages that result in the release of signal and transit peptides and the initiating methionine have been automatically collected from the annotations in the SwissProt protein sequence database. However, cleavages were not previously assigned to a specific MEROPS identifier. This has now changed, and assignments made where possible. Such assignments can only be made for organisms where the genome has been completely sequenced and only one homologue is known from the family in question. Data for the cleavage position is usually determined by N-terminal sequencing, but readers should be aware that at least for chloroplast transit peptides, aminopeptidases are also transported into the chloroplast which may remove amino acids from proteins subsequent to the removal of the transit peptides.

Pharma pages
For peptidases that are drug targets we are now collecting links to databases of interest to the pharmaceutical industry. These are collected together on the new Pharma pages accessible for the peptidase summary. We are currently making links to the PubChem BioAssay database and the Binding Database.

Literature flags
Several new flags have been added to the Literature pages. The full list of flags is:

A Assay method,
E recombinant Expression,
I design of small-molecule Inhibitors,
K gene Knockout or other artificial genetic manipulation,
M natural Mutation, allelic variant or polymorphism,
P Substrate specificity,
R RNA splice variation,
S three-dimensional Structure,
T proposed as a therapeutic Target,
U suggested to have therapeutic potential itself,
V Review.

Structure pages
Structure pages now include a link to Proteopedia.