I'm doing the homology modelling using YASARA for my protein (it's a DNA polymerase from geobacillus). The model show the front tail after I adding the amino acid myself which was belong to my protein, but not included inside the model. I have tested the front tail using SignalP software and show up not the signal peptide. Do anyone know what is that?
First guess after looking at this: Yasara did not model this part or the protein.
I assume that the 3D structure that was used as template is just shorter than the sequence information you gave as input.
This can happen for example if you submit the whole sequence of a protein which contains several domains (ex: a catalytic domain + a dimerization domain), while only a single domain of the protein was crystallized in the case of your 3D template.
This should be apparent from your alignments and from the information you can get about the 3D template.
YASARA is not used for homology modeling. In fact it is a viewer which works according to PDB file and the coordinats in that file. Since there is no coordinats it is unable to recognize the structure.
You first have to use software such as MODELLER and add your tail there to be able to view it in the correct form.
Be aware that YASARA is not the right software for this purpose.
hello Alex! what did you do to model your sequence in Modeller? could I have a look on alignment and script files?
in fact, i don't see any reason to use pdb95.pir files since you can use BLAST to find a template and then to download it from PDB (which is rapidly growing, thus i don't know if the best template would be listed in pdb95.pir) and align sequences manually in a reasonable time.
Homology modeling EXISTS in YASARA, but in Yasara Structure version, not in YASARA View
Best regards, Azat
Hi Azat, the model that I obtained from Modeller having a very poor quality (after I had verified using Verify3D, Ramachandran plot and Errat) as compared to the one using Yasara. And yes, I'm using YASARA structure, not yasara view. The structure are total different even I had tried to superimpose both structure from different software. The quality for yasara model (shown in above) had better quality, reach up to 90%.
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