Protein structure prediction using PSSM? Or not?
I think you are making PSSMs out to be much more sophisticated than they really are.

A PSSM is merely a scoring matrix — it gives position specific scores for each residue at a given location.

There is no explicit pairing of interacting residues though that does sound like an interesting approach ...

You can learn more about PSSMs from many sources on bioinformatics including NCBI.