Folks,
I have modeled some dimers of a large protein and a much shorter partner (~350aa for X and about 80aa for Y) . There are crystal templates for such dimers. The best resolution structures have different large and small proteins. So I have templates with X'Y' and X''Y''. X' and X'' are homologs as are Y' and Y''. The Y family is quite variable in length. When homologs from distant organisms ( eg plant, fungi, fish mammal) are aligned there are gaps compared to the mammalian templates.
In mammals X' and X'' are in related but distinct clades. If I model a yeast X protein to each mammalian template can I say that the yeast protein is better represented by one or the other template based on a DOPE score? ( the GA341 scores are not helpful since they are always 1.000 for these models)
This is several questions I guess. 1) Are DOPE energies normally distributed? Could I statistically compare DOPE scores of models made with one template to those from another template. 2) I have some evidence that longer XY pairs have "better" DOPE scores than shorter pairs. Is there a statistical way to control for "length"? 3) I was just looking at DOPE scores for two models. One with from an alignment with gaps and the other from an alignment without gaps. The PDB model files are different sizes yet the scores are identical. Does DOPE ignore regions that are not in the template?
Starr