Hi Sadaf,
I would start with BRENDA ( http://www.brenda-enzymes.org/ ) for an overview on the protease. The web servers and databases that you should consider will be highly dependent on the details of your particular structure. I put together a list of some programs/servers/databases that you may want to consider ( http://bit.ly/d2I11n ). I hope it helps.
Take Care,
Sean Seaver
P212121
http://store.p212121.com/
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