what is the easiest option (a server or software) to compare two (multi-domain) proteins that lack any considerable sequence identity, but look quite similar (at some parts, i.e. domain 1 and domain 2 of protein A look very similar to domain1 and domain 2 of protein B but the inter-domain linkers in protein A and B are very different)? I can  cut domains manually in pdb files and superpose them, but there are many more domains and probably there is a more elegant way.

Thank you for your suggestions,

With kind regards,

Albert