Assuming you have your structure as a pdb file and your sequence in a fastA file:

Homology modelling - in this process, you assign an altered sequence to a given backbone structure e.g. using Modeller https://salilab.org/modeller/, most easily used in conjunction with ChimeraX https://www.cgl.ucsf.edu/chimerax/. You'll want to set this up in a manner that you give the program your structure as the only template and alignment, and not allow it to search the database for an alternative template or sequence to structure alignment.

You can, of course, also script the PyMol mutagenesis tool to assign the sequence to the structure, but this does not do anything to adapt the side chain rotamers, therefore I expect you would get a mess of clashes even if you mutate every amino acid in a natural structure to its own sequence. For a residue-by-residue sequence assignment with side chain extensive rotamer optimisation, you might consider Rosetta FixBB https://www.rosettacommons.org/docs/latest/application_documentation/design/fixbb.

As someone who has done a lot of protein design before I retired, I would certainly be interested in seeing the results you are getting!

Professor Annemarie Honegger , thank you so much for your detailed reply! I really appreacite your help. But I have one more question to you: do you know any useful tools (other than ANARCI, it couldn't recognize non-native Abs) to determine CDR regions of non-native antibody (designed one)?

Alternatively, you can use other software tools like UCSF Chimera or MODELLER to merge the sequence and structure. The specific steps may differ depending on the software tool you use.

Currently, the SAbPred is the best place for anything antibody related. However, CDR definitions are based on the conserved features of natural antibodies, e.g. CDR boundaries are defined relative to the highly conserved disulphide Cys, core Trp and Gly-X-Gly beta bulge positions or at least require an unambiguous sequence alignment. So, depending on how far the sequence of your designed antibody deviates from natural sequence, you may have to do a structural alignment of your construct to natural antibody variable domains and copy over the CDR boundaries from there.

Basically, CDR definitions were originally bases on the sequence variability of natural antibody sequences, and confirmed by antigen contact probabilities derived from antibody-antigen complex structures.

Check out https://plueckthun.bioc.uzh.ch/antibody/Numbering/index.html and linked pages e.g. "Standard Header", where you can see how the CDR boundaries relate to antigen contact probabilities derived from the structures of hundreds of antibody-antigen complexes See: https://plueckthun.bioc.uzh.ch/antibody/Structures/AgContact/index.html

(published in Honegger&Plückthun, J.Mol.Biol. 309 (2001) 657-670 https://plueckthun.bioc.uzh.ch/antibody/Publications/PDF/JMB309_2001_657.pdf

Mohammed Almajidi , ChimeraX https://www.cgl.ucsf.edu/chimerax/ is the successor of UCSF Chimera.

"Please note that UCSF Chimera is legacy software that is no longer being developed or supported. Users are strongly encouraged to try UCSF ChimeraX, which is under active development." https://www.cgl.ucsf.edu/chimera/

Mohammed Almajidi, hello, thank you for your answer! Could you please explain how it might differ and can you provide specific examples for it?

Homology Modelling 2020 Tutorial - UCSF Chimera and Modeller

https://www.youtube.com/watch?v=HUSQnIiY7sE

From the ChimeraX Documentation:

https://www.cgl.ucsf.edu/chimerax/docs/user/tools/modeller.html

Annemarie Honegger Professor thank you for everything: one more question: do you know any good tools for plotting datasets as a distribution curve (I just wanted to show Rosetta score distibution of my designed antibodies)?

I just use EXCEL for the purpose

https://support.microsoft.com/en-us/topic/create-a-histogram-in-excel-a15d4de8-a432-72cd-9434-1a7f3e88698e

Professor Annemarie Honegger, I have a very important question:

I obtained a Rosetta score for my antibody-antigen complex (which is a ground truth since it is a stable structure and experimentally determined by Cryo-EM), so the total energy score equals to +628 (positive score). The thing is I calculated this score with the help of online docking server called "Rosetta Dock" or "Rosie" - https://rosie.rosettacommons.org/docking2, but I dont know how reliable it is...and is it a mistake by server, although I measured the energy quite few times?? Should I score by regular rosetta in my own local server???