Rosetta reference energy

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    • May 7, 2012 at 2:56 pm #1270
      Anonymous

        Dear ALL,
        Does rosetta has secondary structure dependent reference energy? By the way, how do I get the 20 reference energy values (if there are not secondary structure dependent reference energy )? Thanks very much!!

      • May 7, 2012 at 3:11 pm #7073
        Anonymous

          Hi Lindsay,
          The reference energy is only dependent on sequence. The reference energy for each amino acid is stored in the .wts file for the scorefunction. Not sure on the order of amino acids corresponding with the refs, but I will see if I can find it.

          -J

        • May 7, 2012 at 9:15 pm #7080
          Anonymous

            The reference energies have been reweighted repeatedly.

            I also agree that it’s in order by single letter code.

            The reference energy is not sensitive to secondary structure. The p_aa_pp term, probability of a residue type given phi and psi, may be what you are looking for.

          • May 7, 2012 at 9:52 pm #7081
            Anonymous

              The reference energies, as Steven pointed out, depend only on the amino acid composition and do not depend on the secondary structure. There are other components of the energy function that are aware of secondary-structure, for example the p_aa_pp term, and the hydrogen bonding term (which prefers that the backbone groups form hydrogen bonds). Fragment selection for abinitio and other low-resolution protocols also helps build-in secondary structure. There are other low-resolution secondary structure terms as well: rsigma, sheet, hspair, and sspair.

              Rocco is correct: the 20 reference energies are given in order by 1-letter amino acid codes: ACDEFGHIKLMNPQRSTVWY

            • May 7, 2012 at 3:18 pm #7074
              Anonymous

                here is what I found
                METHOD_WEIGHTS ref 0.1544 -0.1396 -0.4716 -0.6336 1.2214 -0.1386 0.9844 0.4794 -0.4596 0.2824 -0.2666 -0.7886 -0.8316 -0.7706 -0.7726 -0.2696 -0.2486 0.3544 1.3524 0.9624
                but these are the weights, not the reference energy.

              • May 7, 2012 at 4:04 pm #7076
                Anonymous

                  Regarding order, unless I’m completely misremembering, it’s alphabetical by one-letter code (So: Ala, Cys, Asp, Glu …)

                • May 7, 2012 at 3:32 pm #7075
                  Anonymous

                    These should be the energy for each AA. The weight of ref in score12 is 1, the ref energies are optimized for each scorefunction in use…checkout Rohl 2004 in Methods of Enzymology or the original Kuhlman paper describing ref, ‘Native protein sequences are close to optimal for their structures’ (2000). Hope that helps.

                    -J

                  • May 7, 2012 at 4:24 pm #7077
                    Anonymous

                      Thank you

                    • May 7, 2012 at 5:57 pm #7078
                      Anonymous

                        Hi,
                        I check the paper’s supplementary, the Wref(Ala) is -0.93. It is not the same as what I found in the score12_full.wts
                        METHOD_WEIGHTS ref 0.16 1.7 -0.67 -0.81 0.63 -0.17 0.56 0.24 -0.65 -0.1 -0.34 -0.89 0.02 -0.97 -0.98 -0.37 -0.27 0.29 0.91 0.51

                      • May 7, 2012 at 10:22 pm #7082
                        Anonymous

                          Got it. Thank you!

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