I am looking for an approach and or tool/software by which I could link one protein domain to another protein domain via linker (24AA and Gly rich linker)?
By "PSIPRED" server in UCL, you can do it. 2 dimensional structure of the protein could be predicted by PSIPRED. After pasting the sequence, click "DomPred" too. If you click "BioSerf" 3D modeling may be possible too.
@Jonathon: I was wondering to do same. I make linker in pymol (builder tool), moleman for renumbering and Coot for attaching linker at appropriate position.