How can move peptide on cleft of enzyme on Flexpepdock?

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    • June 5, 2014 at 9:22 am #1905
      Anonymous

        Hello everyone,

        I try to find where is the binding sites of peptide (7 amino acid) on enzyme. And I run Plexpepdock (Rosetta 3.4) . I do not have any informations and the binding site and the backbone of peptide (I just have the sequence).
        The fisrt time, I try to move peptide on cleft manually and chose the structure have lowest score. But, I think this is not a good way to cover all the cleft of enzyme by peptide.
        Do you know any command line I need to add on the flags which can help peptide move or if any programe can generate coordinates of peptide automatically which can cover cleft better.

        Thank you so much
        I m waiting your reply.

      • June 5, 2014 at 9:51 am #10080
        Anonymous

          Hi,
          FlexPepDockAbinitio can sample extensively when the peptide is placed in the binding site. If you don’t have info regarding binding site I will recommend you to use PeptiMap ( http://peptimap.bu.edu/ ) to predict the binding site and then manually place the peptide in the binding site and run FlexPepDockAbinitio. Don’t use refinement only protocol as extensive sampling is needed. Let me know if you need help with this.
          FYI: We are currently working on incorporation of binding site info in the docking protocol. This will allow efficient use of the predicted binding site.

        • June 10, 2014 at 11:11 am #10089
          Anonymous

            Thank you so much nawsad!

          • December 23, 2014 at 2:38 am #10718
            Anonymous

              Dear nawsad,
              In my case, I know the binding site and I have the crystallographic structure of a reference peptide located at the binding site, but I need to generate several (thousands) of other linear peptide structures at this same binding site, in order to run the docking calculations.
              Any tips on how to make automatic the generation of the linear peptide (from sequence of residues), and the positioning at the region of the binding site (maybe alignment with the crystallographic structure of reference peptide?) ?
              Thanks in advance for any help.
              Best Regards.

            • January 2, 2015 at 1:38 pm #10724
              Anonymous

                Dear nawsad,
                In my case, I know the binding site and I have the crystallographic structure of a reference peptide located at the binding site, but I need to generate several (thousands) of other linear peptide structures at this same binding site, in order to run the docking calculations.
                Any tips on how to make automatic the generation of the linear peptide (from sequence of residues), and the positioning at the region of the binding site (maybe alignment with the crystallographic structure of reference peptide?) ?
                Thanks in advance for any help.
                Best Regards.

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