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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.

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  • $\begingroup$ You have distance between alpha carbons or beta carbons (or other atoms of the residues)? Usually a threshold is set because below certain measure it can't be and above certain threshold it doesn't mean a contact between the residues. Do you have any other information besides the distance matrix, like the sequence of the protein? $\endgroup$ – llrs Nov 26 '18 at 8:55
  • $\begingroup$ @llrs They are only carbon alpha distances and I want to reconstruct the backbone with carbon alphas and no more atoms.No more information, just the distances between carbon alphas for each residue. $\endgroup$ – Wise Nov 26 '18 at 16:17
  • $\begingroup$ You could use the multidimensional scaling approach, but I suspect it might propose invalid angles between the backbone. It would be possible to use it as a starting point before checking the angles between the backbone. But I don't know if there is any software to do this (it is a strange problem to have), or either you know the sequence or the sequence and the structure, but just the distance is strange. $\endgroup$ – llrs Nov 27 '18 at 9:50
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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.

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