Try Swiss Model. https://swissmodel.expasy.org/

You don;t have to worry about the template, in case you do not know.

But if you do know the template and need more acurate results, maybe try I-TASSER. https://zhanglab.ccmb.med.umich.edu/I-TASSER/

Most tags do not have a defined structure in solution, but are flexible. Occasionally you get density for a tag in an X-ray structure, mostly because the tag is immobilized in a crystal contact. You can just model your sequence including the tag, but remember, that you are getting is at best one of many conformations forming the conformational ensemble in solution. Most modeling servers will return multiple solutions which will differ in the conformation of the tag.

Thank you very much so far, Mrs. Honegger and Mr. Bansal.

I have already tested SWISS model which unfortunately excluded the tagged sequence from the model. The terminii of my template seem to define my "borders".

Regarding your comment about the flexible tag, I am aware of that there is no "ideal" conformation of the tag sequence. I was just hoping to reveal that the tag is not buried within the structure.

Thus I was hoping to receive a model which kind of simulate a potential tag sequence and returns my wildtype structure of the core sequence.

You can try to seek for the given peptide sequence in RCSB database. There, there is a sequence searching tool, but the peptide has to go above a minimal size. You might be lucky and get an structure with your peptide modeled.

However, as mentioned before by Mme Honegger, these tags are often flexible and when visible, the conformation relies on specific contacts with the rest of the protein (which in your case will be different). That to say that the precise conformation that you'd get is relatively meaningless. In the end, tags are in majority of cases flexible and floating around.

You are not going to see if the tag is buried within the protein by homology modeling even if it were, unless such a situation had been previously observed crystallographically - for that, you would have to do an ab-initio folding simulation.

Most likely, if your tag were to be buried within the structure (interact with folding intermediates), the rest of the structure would not fold properly and you would get an aggregated mess upon protein production. If you model your protein for an illustration, just annotate "x amino acids unstructured". If you need your tag in, e.g. for MD analysis, just model your tag as extended, run a few rounds of simulated melting and annealing on it and then merge one of the reasonable results with the rest of your protein.

Do you have any recommendation for a tool which allows the merging/docking of my "native" protein (solved crystal structure) with my modelled peptide structure?

I did the modelling of my tag and I received some reasonable structure, but now I need to do a good merging.

Thank you!

Well, depending on the tag, it may simply be intrinsically disordered with multiple changing conformations. Which modeling approach you use varies widely depending on what kind of question you are trying to answer. If you feel you have a reasonable starting point for your tag's structure, the best approach sounds like it would be molecular dynamics-based time resolved equilibration, though that can be biased significantly on your starting position, so to do a thorough job might require more resources than it's worth.

Ok, I get the point and I am aware of that there no perfect/final conformation. Since the peptide tag is only 19 AA long and the repetitive AEAAAA-motif should form helical structures, I am pretty sure that the modelling performed with PEP-FOLD3 is roughly sufficient for my purpose. The challenge I have only little experience of is the merging of this model to the C-terminus of my wild-type protein structure.

So far, I managed to combine simply the 2 pdb-files using the "Build"-function in Chimera. However, this method does not take into account surface charges or other interactions between protein and peptide, but it just forms an artifical peptide bond. Maybe there is some (simple) tool to which I add both pdb-files and it creates a potential orientation of the tag relative to the wild-type protein structure.

Ah, in that case honestly your best bet is to simply look. "Pick up your visual scanning". You have a small helix with 4 negative charges including the C-terminus. When you look at the structure of the protein it's bonded to, do you see a large number/cluster of positively charged residues nearby? Is there a large hydrophobic patch that could interact with the alanines? If not, then it's a safe bet that the tag is not interacting with the protein.