Proteomics on Public Galaxy Servers

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Proteomics on Public Galaxy Servers

Dave Clements
Hello all,

There was something buries in the October Galaxy Update newsletter that just went out that might be of interest to this group.  One of the new public Galaxy servers has several proteomics tools on it:


Laboratory of Biological Physics at USP-FCFRP
  • Link:

  • Domain/Purpose:

    • Summary of the currently available tools:
      • ProtPred-GROMACSAb initio protein structure prediction framework which uses evolutionary algorithms to optimize objective functions such as potential energy, number of hydrogen bonds and solvent accessible surface area. 

        • 2PG: Faster and simpler algorithm in which one objective function is optimized
          3PG: A more robust approach in which multiple objective functions are optimized at the same time

        Protein Validation: Check the integrity of a PDB file
        Protein Desolvation: Remove a solvation layer around your protein.

  • Comments:

  • User Support:

  • Quotas: 

    • "You can use tools developed at our laboratory and by our colaborators for free. You just need to sign up to the server using your academic e-mail."
  • Sponsor(s):

And, while I'm here, there are also a couple of other public sites that feature proteomics prominently:

  1. Galaxy-P
  2. GWIPS-viz
  3. SymD (not up currently)
Hope this interesting.  If it isn't, please let me know.


Dave C

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