Profisis prediction (ISIS server ) - help

[Luke Nitish]

Hi,

I'm working on research related to protein-protein interactions, and i use the ISIS server to predict hotspots.
For my research i need to predict hotspots for lot of proteins (for thousands in my data set) and i downloaded the virtual image(http://www.predictprotein.org/) and tried to predict hotspots, it works;
but for every prediction we need three files (.fasta, .hssp, .rdbProf) and its not feasible to do it for lot of protein sequences.

can anyone help me to find a way or give some advice on how to get hotspot predicted for lot of proteins( in a single fasta sequence file)

Thank you in advance

hoping some guidance

Luke Nitish

University of Colombo School of Computing
lukenitish.co.nr