Does linker modeling exist?

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    • February 22, 2012 at 3:34 pm #1169
      Anonymous

        Hi! Is there an existing application that will model a linker (fragment based) between two protein domains, and at the same time ensure that one domain does not clash with the other one? If there is such a thing can someone provide an example/command line etc. ?

        Thanks in advance,
        Aroop

      • February 22, 2012 at 4:05 pm #6675
        Anonymous

          FloppyTail will do it. The trunk version has more features than the 3.3 release, if you still have access to it (assuming you’re the Aroop I think you are). http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/d8/d39/_floppy_tail.html This appears to be the live trunk user guide rather than the static 3.3 guide, if you are using 3.3 you’ll want to read the embedded documentation instead.

          There is also an unreleased application “multidomain_switch” that does domain assembly in trunk, and a third application assemble_domains_jd2 that I have no idea what it does.

        • February 28, 2012 at 8:47 pm #6714
          Anonymous

            This is indeed the Aroop that you thought I was. However, I am no longer in Jeff’s lab and hence do not have access to the trunk. I can only depend on release versions. I will look into the userguide that you have pointed me to and let you know if I have further questions. Thank you.
            Aroop

          • March 6, 2012 at 7:51 pm #6758
            Anonymous

              Thanks Steven,

              I found FloppyTail in the scenarios section of Rosetta 3.3. As I had mentioned I am trying to model a linker between two domains, where the C-terminal domain will move around based on the linker conformation. To that end I am using the following command line:

              /Users/aroop/rosetta33/rosetta3.3/rosetta_source/bin/FloppyTail.macosgccrelease -database /Users/aroop/rosetta33/rosetta3.3/rosetta_database/ -s inpt.pdb -mute core -flexible_chain H -flexible_start_resnum 211 -flexible_stop_resnum 217 -in::file::frag3 aainptH03_05.200_v1_3 -nstruct 3

              However, I find that only one the entire linker (which was originally extended) was not randomized by fragment insertion. Only one fragment had been inserted in each model, i.e. the models are different, but they have only one fragment difference from the starting structure. Am I doing something wrong? Is there a flag to select the number of fragment insertion to completely randomize the linker?

              Thanks once again,
              Aroop

            • February 28, 2012 at 9:57 pm #6715
              Anonymous

                I’ll get you a copy of trunk FloppyTail if you need it, let me know. We’re close to 3.4 anyway.

              • March 6, 2012 at 7:57 pm #6759
                Anonymous

                  You haven’t passed any flags controlling how many Monte Carlo cycles are run. It is just running default test-length runs, probably, and only has time to perform one insertion. (Also, on a region that short, how do you know how many fragments are inserted?). Take a look at the flags in the integration test and dox file.

                  http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/d8/d39/_floppy_tail.html

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