Hello
May i ask you about using Modeller for making 3D model fussion protein. I want to build a fusion/chimera protein structure which is including 2 different protein and then evaluate quality of fusion protein 3D structure. I want to use modeller or any other suitable software for this purpose, How can I do that?
Thank you
First get the structure or model each domain separately. The relative orientation of the two domains in the fusion protein depends on and/or informs the design of the linkage: If you add a flexible linker, the relative domain orientation is flexible. If you want to design a minimal linker or a rigid connection, you will need to interactively move the two domains into the relative orientation you wish to achieve, ensuring that you have no clashes, then determine the linker length you need to close the remaining gap (or the number of flexible residues you need to delete from the termini for a minimum length connection).
You can then export the two domains in their designed relative orientation with the same chain label and non-overlapping residue numbers, export them as one pdb file and use this as a template for modeller.
e.g. see:
Article DARPin-Based Crystallization Chaperones Exploit Molecular Ge...
https://plueckthun.bioc.uzh.ch/wp-content/uploads/Publications/APpub0409.pdf
for rigid connection, https://plueckthun.bioc.uzh.ch/wp-content/uploads/Publications/APpub0346.pdf for a minimal length linker.
You can then optimise the sequence of the linker region, e.g. using rosetta FixBB
Thank you, Mrs. Annemarie Honegger . It is very helpfull information. I will try it, Thanks
Regards
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