PACMANS: Protease-Ase Cleavages from MEROPS ANalyzed Specificities

PACMANS is software using a bioinformatically informed algorithm to predict, design, and disrupt protease-on-protease hydrolysis. This program uses a substrate protease's amino acid sequence and a protease-ase's specificity matrix from MEROPS to produce a ranked list of the most likely hydrolyzed segments of the substrate protease's amino acid sequence. This program is currently implemented in a downloadable MATLAB Application (below) and will soon be available online through this website for users without access MATLAB.

This work has been published by Ferrall-Fairbanks et al in Protein Science.

PACMANS software

Requirements:

Installation Instructions:

  1. Install Matlab.
  2. Run PACMANS.mlappinstall as an executible.
  3. Matlab will open and install PACMANS into the Matlab apps tab.
  4. Click the new PACMANS button to start the gui.

PACMANS is tested on Windows and Mac OSX, but should work on Linux with Matlab.

DOWNLOAD

The sofware can be downloaded as a Matlab App Installer

Example:

Here is an example described in Ferrall-Fairbanks, Platt et al.

  1. Protease-Ase: Cathepsin S
  2. Substrate Protease: Cathepsin K
  3. Cathepsin S MEROPS link: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=C01.034;type=P
  4. Cathepsin K Amino Acid Sequence:
    MWGLKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPLSHSRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
  5. OUPUT:
    • Histogram figure opens automatically when run is completed
    • Text file is created in current folder with full ranked list of sequences

Usage Instructions:

  1. Launch PACMANS app within Matlab.
  2. Choose a Protease-ase name and substrate name. These names are used to name the output file.
  3. [Optional] Choose a pocket size. Defaults are 1-8.
  4. Navigate to MEROPS and choose a protease-ase that has a specificity matrix. From the example above, find the link to the specificty matrix of cathepsin S http://merops.sanger.ac.uk/cgi-bin/pepsum?id=C01.034.
  5. Enter the amino acid sequence of the substrate. This sequence must be in FASTA format without any spaces. These sequences can be obtained from Uniprot.




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