Reconstruct a protein's 3D structure from a pair-wise distance matrix What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues?

I think the question is self-explanatory. I know of this method 
but it seems that it uses contact maps, which actually use a certain cut-off. I don't have a cutoff based contact matrix but a matrix with actual distances.
Finding coordinates of N points that preserve (as well as possible) pair-wise distances from an NxN matrix is called multidimensional scaling.

But I don't enough about the context of your problem to tell if/how it is applicable.