secondary structure prediction for generation of fragment libraries

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    • June 25, 2011 at 7:47 am #962
      Anonymous

        I found that the “psipred” installed at three different places generated different results for one sequence (Rad59, please focus on the 40 aa at its N-terminus). Is that because their version? Which “psipred” is more reliable?

        1. “Fragment Libraries” server (v2.6): http://robetta.bakerlab.org/downloads/fragments/22521/
        2. the SYMPRED server (v ?): http://zeus.few.vu.nl/jobs/aeb9f401c184595c85e6ef7aaef6defe/
        3. A local installed Psipred copy (v. 3.2 ?).

        The secondary structure prediction will affect the fragment libraries. How much do the fragment libraries affect the final AbinitioRelax prediction?

      • June 27, 2011 at 2:25 pm #5817
        Anonymous

          ‘Which “psipred” is more reliable? ‘

          This is really a question for the developers of psipred more than us. I would hazard a guess that the most recent version is “best”.

          I think the secondary structure libraries matter quite a bit to the final result. I’m not aware of anyone benchmarking slightly-different fragment inputs for folding a known structure to see which one comes out best.

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