Excellent tool for prediction of the potential cleavage sites for MMPs

Scientists of Sanford Burnham Medical Research Institute (La Jolla, CA, USA) recently announced the opening of a new web server providing excellent tool for prediction of the potential cleavage sites for matrix metalloproteinases (MMPs).

The server is capable to predict cleavage positions for 11 human MMPs: MMP-2, -3, -8, -9, -10, -14, -15, -16, -17, -24, -25, for which statistical profiles have been derived based on high throughput phage display experiments. The server accepts the structure data (in PDB format), the sequence data (in FASTA format) or UNIPROT id of putative protein target as an input and produces information about the position of tentative cleavage sites.

The server additionally provides other available information for your input protein:

  • Co-localization and co-expression of the input protein and its processing MMP
  • Positions of post-translational modifications (PTMs), and Single Nucleotide Polymorphism data (SNPs) that could interfere with the cleavage event (the information about the disease related SNPs is also provided if available)
  • Signal peptide and secondary structure, solvent exposure and transmembrane domain(s)
  • VMS - virtual mass spectroscopy (the server produces ordered mass spectrum of expected mass fragments based on the position of tentative cleavage position, which would be very helpful in interpreting experimental MS data).
  • Server matches the structure to your input protein sequence and displays potential cleavage sites, PTMs and SNPs mapped on this structure.

For more information please visit: http://cleavpredict.sanfordburnham.org. But, if you have any specific questions or need more information, you can directly contact Dr. Piotr Cieplak by e-mail: pcieplak@sanfordburnham.org

 

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