I have generated a model using EasyModeller and following so I have generated a DOPE profile using the model and template. Pink line indicates the model and the orange line depicts the template. Based on the DOPE profile, it was observed that there are conserved regions between residues 250 and 280 and at 380 to 390. However, these residues are not highly conserved.
Now, are there any more conserved residues in the model? I might be wrong here. Any response would be appreciated. Thank you.
In order to find out conserved residues between two proteins one needs to do pairwise alignment of the two protein sequences, and not compare the DOPE scores from MODELLER. The DOPE profile can be used to compare the fit of the 3D model across the regions of high and low sequence conservation.
Your DOPE profiles should make more sense to you if you divide the alignment position region into areas of high and low conservation.
Hi Dibyendu,
Thank you for your response. What do you mean by dividing the alignment position region into areas of high and low conservation?
The X axis of your graph is alignment position which corresponds to the amino acids of the protein. So first do a pairwise alignment of your template to the sequence to be modelled and based on that find out regions of that are conserved or not (high or low). And using this knowledge look at the DOPE profile now. If now the regions which are highly similar or identical have a similar or close dope profile, and other regions not so much, then you may assume that the model is properly aligned and is good.
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