Click on the type of Protease Database you want to use :
Octapeptide or Tripeptide (currently in use)

Enter the PDB ID :

Once you enter the PDB ID., the program will scan the protein sequence with a list of cleavage sites of proteases obtained from Merops database. There are two options provided for the cleavage sites namely octapeptide (P4P3P2P1-P1`P2`P3`P4`) and tripeptide(P3P2P1) .Putative substrates thus obtained are passed to a program called POPS to calculate accessible surface area values. These values are then converted to relative solvent accessible surface area values and the output will be available in csv formatted file.Once the job is complete ( the loading of the page stops and the PDB id disappears), you can view the results by clicking on the results button. For more please visit the help page.



Reference:
Prasanna Venkatraman, Satish Balakrishnan, Shashidhar Rao, Yogesh Hooda and Suyog Pol. A Sequence and Structure Based Method to Predict Putative Substrates, Functions and Regulatory Networks of Endo Proteases. PLoS One, 2009.

 

 

 


A tool by Satish Balakrishnan & Suyog Pol
Prasanna Lab