RosettaDock with loop rebuild HOWTO ?

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    • June 4, 2009 at 4:12 pm #481
      Anonymous

        Hi,

        we are trying to dock two partners, and we want to rebuild a loop of one of the partners. We searched into the README.pose_docking file, and we found:

        extract from the README

        D. To perform a small perturbation docking interating between loop
        rebuiding and docking. Brief, the protocol will first remove the defined
        loops from the complex, and then carry out low-resolution docking
        without those loops. Afterwards, the loops will be rebuilt onto the
        docked model in the low-resolution and the full-length model will
        undergo fullatom docking rigid-body refinement and loop refinement.

        $> rosetta.exe aa 1brs 1 -s 1brs.rlx -dock -pose -loop -fast -dock_mcm -dock_pert
        8 8 8 -unboundrot -dock_rtmin -ex1 -ex2aro_only -find_disulf

        end of the extract


        We tried these options, but rosetta crashes with this message:

        >WARNING!! .dat file not found!

        >Looking for fasta file: ./mod1_.fasta

        >fasta file not found!

        >setup_protein_sstype: query sequence not defined !!!

        >fasta file needed to read in psipred prediction !!!

        >query sstype will not be defined in this run !!!

        we went a bit further adding the -use_pdbseq, but now it crashes with this message:

        >[T/F OPT]Default FALSE value for [-handedness_score]

        > DAMN: read_fragments can’t locate ./aamod1_03_05.200_v1_3

        What are we doing wrong ? BTW, we were able to run loop minimization example C in the same README.pose_docking file, using:

        $> rosetta.exe aa 1brs 1 -s 1brs.rlx -dock -pose -loop -minimize_loop
        -dock_mcm -dock_pert 8 8 8 -unboundrot -dock_rtmin -ex1 -ex2aro_only
        -find_disulf

        by appropriate definition of the [start].pose_loops file.

        Any help really appreaciated, we are stacked here since a few days…
        Luigi

      • June 10, 2009 at 3:42 pm #4095
        eprocko
        Participant

          It looks like you need to generate fragment libraries using the Robetta server. Place all output files into your working directory. Rename the 03 and 09 libraries to:

          aa1brs103_05.200_v1_3 and aa1brs109_05.200_v1_3

          It appears that these are not included in the tutorial. Rosetta documentation is notorious for being incomplete and confusing….

        • June 19, 2009 at 7:30 pm #4104
          eprocko
          Participant

            One thing I have learned is that in order to use -pose -loop during docking, is that one must submit a .fasta sequence containing both the protein 1 and protein 2 sequences when generating fragment libraries. This is not obvious. In addition, those sequences must be continuous (as if there were 1 sequence) and the number of residues in this “single” sequence must correspond exactly to the number of residues in the .pdb file.

          • June 29, 2009 at 7:34 pm #4105
            sokrypton
            Participant

              Hi mchldln, I have a question about your second reply post. If the .fasta sequence containing both protein 1 and 2 when uploaded to generate the fragment libraries. And if they have to be continuous, which seems really odd to me, will the docking-loop modeling still work appropriately if you feed it this weird fragment libraries? I mean, how does rosetta distinguish between those two separate subunits?

              I have read several of your posts, and it seems to me that you have a lot of “trial and error” experience in using Rosetta 2.* version, which is very valuable, given the incomplete Rosetta documentation.

              Thanks!

            • July 6, 2009 at 5:52 pm #4109
              eprocko
              Participant

                Hi mdyini,

                The only way I could the loop modeling and docking to work simultaneously is to have the “correct” fragment library files. The only way I found to obtain the correct files was to merge both fasta sequences into one continuous one. Yes this seems odd, but it works for me. The other part of the puzzle is to have both proteins in the .pdb file with continuous (at least unique) numbering.

                Results so far have been expected.

                Initially, I generated frag libraries for one of the proteins by submitting only its fasta sequence. Libraries were generated, but they were rejected by rosetta (even though I only wanted to flex loops in this one protein).

                Ultimately, I was able to flex loops in both proteins while docking using this method.

                In summary, my pdb has two proteins numbered 29-342 and 400-505. I have a fasta file containing 328 residues, all in a “single” sequence, of which I submitted to Robetta for library creation.

                Let me know if I can add more details. Yes, I’ve spent a good bit of time with trial and error :)

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