Answers.Body: <p>Finding coordinates of N points that preserve (as well as possible) pair-wise distances from an NxN matrix is called <a href="https://en.wikipedia.org/wiki/Multidimensional_scaling" rel="nofollow noreferrer">multidimensional scaling</a>.</p>
  
  <p>But I don't enough about the context of your problem to tell if/how it is applicable.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-24T21:47:58.860Z
Answers.LastActivityDate: 2018-11-24T21:47:58.860Z
Answers.UserDisplayName: marcin
Body: <p>What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues?</p>
  
  <p>I think the question is self-explanatory. I know of this <a href="https://academic.oup.com/bioinformatics/article/31/21/3499/194596" rel="nofollow noreferrer">method</a> 
  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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-26T08:55:45.497Z
Comments.Text: 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?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-26T16:17:36.487Z
Comments.Text: @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.
Comments.UserDisplayName: Wise
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-27T09:50:31.287Z
Comments.Text: 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.
Comments.UserDisplayName: llrs
Tags: <pdb><protein-structure><3d-structure>
Title: Reconstruct a protein's 3D structure from a pair-wise distance matrix
ThreadText: # Reconstruct a protein's 3D structure from a pair-wise distance matrix
  
  (Asked by: username_0 on 2018-11-24)
  
  What is a good method to reconstruct a protein's 3D structure from a pair-username_0 distance matrix of residues?
  
  I think the question is self-explanatory. I know of this [method](https://academic.oup.com/bioinformatics/article/31/21/3499/194596)
  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.
  
  **Tags:** pdb, protein-structure, 3d-structure
  
  > **Comments:**
  > **username_1**: 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?  
  > **username_0**: @username_1 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.  
  > **username_1**: 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.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-11-24. Score: -1
  
  Finding coordinates of N points that preserve (as well as possible) pair-username_0 distances from an NxN matrix is called [multidimensional scaling](https://en.wikipedia.org/wiki/Multidimensional_scaling).
  
  But I don't enough about the context of your problem to tell if/how it is applicable.
  
  
  ---
  
  