Hi;

I am looking for a measure to compare the quality of several pairwise protein interface alignments.

assume that I have 4 protein interfaces (A,B,C and D) and I align (A with C) (A-C) and (B with D)(B-D). Mainly RMSD is used for showing how well the interfaces are aligned but the problem is if A and C are around ~7 amino acids and B and D are ~30, then for sure we will get a larger RMSD for B-D.

So what metric can be used to compare between the quality of A-C alignement with B-D?

Thanks in advance;