[DIYbio] Re: Protein Shop Help!

Hi Josiah,

Maybe if I told you what I wanted to do, you could better advise me on which program/s might be better for what I want to do.  I have a target molecule as a substrate.  By identifying several structures in the molecule, I've identified a number of proteins which have substrates which are similar to the structures in my target molecule.  I want to, first, compare the homology of these proteins to find any similar structures.  Second, I'd like to be able to "clip" those similar structures and be able to "paste" them together.  Lastly, I'd like to see how well the "new" protein fits with my original target molecule. I realize that I will probably need several programs to accomplish this, so if you could explain how each program could perform each portion of my process, that would be awesome.

Thanks,
John

On Thursday, September 19, 2013 9:59:12 PM UTC-4, Josiah Zayner wrote:

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:

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