The code appears broke beyond brokenness. The website is down http://proteinshop.lbl.gov/Index.html. I would try emaling Sylvia at SNCrivelli [at] lbl.gov if you really want to try and get it working. However.
-- If you want to do similar stuff I would install VMD http://www.ks.uiuc.edu/Research/vmd/
or pymol: sudo apt-get install pymol
for secondary structure prediction try PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/
And for protein structure prediction use: http://swissmodel.expasy.org/ if it has some homology to some other structure
or http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi if it does not have any homology
for Molecular Dynamics Simulations try namd which comes with VMD or gromacs: sudo apt-get install gromacs
On Thursday, September 19, 2013 7:46:59 AM UTC-5, John Dohnal wrote:
On Thursday, September 19, 2013 7:46:59 AM UTC-5, John Dohnal wrote:
I have never used a Linux OS before, but I downloaded the latest version of Ubuntu in order to run Protein Shop. I downloaded the latest version of Protein Shop, but I don't know how to start it. I know nothing about using Linux, so any explicit, basic instructions would be most helpful. In the readme file, it mentions some other files that may need to be installed, but I don't even know where to begin. Please help!Thanks,John
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