Abinitio Structure Prediction – Sanity Test

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    • #601
      Anonymous

        Short version:

        Is there sequence/structure that would be a good sanity test for a Rosetta 3.1 abinitio structure prediction? That is, I could run through the basic abinitio structure prediction routine and, when I predicted the correct structure, I would know that everything was working properly.

        Longer version:

        Ultimately, I’d like to generate a structure prediction for a 470 residue protein that is predicted to have about seven transmembrane helices. But initially, I’m trying a couple predictions on fragments that are between the predicted transmembrane helices (i.e. predicted aqueous domains).

        I’ve got as far as generating 2,000 structures for a 100 residue predicted aqueous domain using AbinitioRelax and then clustering the structures. But using the default RMSD cutoff of 3.0, I don’t get any clusters (well, all clusters have a size of 1) – and the individual structures I’ve looked at don’t look very realistic: poor packing (not compact) and unrealistic long loops.

        So, there are three general possibilities. First, it may just be that the domain I’m trying to predict doesn’t have the kind of structure that can be predicted by Rosetta. Second, it may be that I’m doing something totally wrong (I’m new to Rosetta). Third, it may be that there’s a bug in Rosetta or in the development environment / compiler that I’m using.

        And so I’m hoping that a sanity test could rule out the last two general possibilities.

        Incidentally, with respect to the third possibility (Rosetta/compiler bug), I notice that there’s a “README.platforms” file that says “Note: GCC with Ubuntu 4.3.2-1ubuntu12 and any version after it does not work”. But I’ve got GCC version “Ubuntu 4.3.3-5ubuntu4” and the Rosetta programs that I’ve needed have seemed to compile and run without error. I should note, though, that I also tried a different compiler, “GCC 4.1.2 20080704 (Red Hat 4.1.2-46)”, and the relax part of AbinitioRelax gives slightly different results. So, I’m not sure if that’s just rounding error or if there’s a bug in Rosetta and/or the compiler.

        Any suggestions/insights will be much appreciated.

        Thanks,
        Westley

      • #4459
        Anonymous

          A) Poke around in the integration tests for abinitio/abrelax. They use 1l2y.pdb, which is a trp-cage, which is conveniently only 20 residues (and thus computes fast). You should be able to use that integration test as a sanity check. (You may need to up the cycle counts from its default state). This is in test/integration/tests/abinitio.

          B) The documentation is probably wrong on exactly which gcc version produces exactly which errors under whichever conditions. I’m pretty sure that line is supposed to read 4.4.1 (and 4.4.1 only). Where did you see that so I can try to fix it? One of our not-so-secrets is that “officially supported” really means “whatever architectures that some developer happens to use” – there are likely to be lots of gaps in our coverage (like, say, most of Windows land).

          C) I don’t know much about it, but there is a membrane_abinitio you may want to consider.

          • #4460
            Anonymous

              > A) Poke around in the integration tests for abinitio/abrelax. They use 1l2y.pdb,…

              Excellent. Thanks! That’s a big help for me.

              > I’m pretty sure that line is supposed to read 4.4.1 (and 4.4.1 only). Where did you see that so I can try to fix it?

              The version of Rosetta that I have came packaged up in “rosetta3.1_Bundles.tgz”:

              ||$ tar tzf rosetta3.1_Bundles.tgz
              rosetta3.1_database.tgz
              rosetta3.1_demos.tgz
              rosetta3.1_fragments.tgz
              rosetta3.1_source.tgz
              BioTools-3.1.tgz
              rosetta3.1_user_guide.tgz
              README.platforms
              README.version
              release.note||

              And the file “README.platforms” contains the following excerpt:

              ||- Linux 2.6.27-9-generic #1 SMP x86_64 GNU/Linux
              Scons script: v0.98.5.r3057
              gcc (GCC) 4.1.1, gcc (GCC) 4.2.4, gcc (GCC) 4.3.2
              Note: GCC with Ubuntu 4.3.2-1ubuntu12 and any version after it does not work||

              > C) I don’t know much about it, but there is a membrane_abinitio you may want to consider.

              I’ll definitely have to give that a try.

              Thanks for all your help on this.

              Westley

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