Body: <p>Hello experts in residue coevolution analysis of proteins,</p>
  
  <p>I am looking for a way to calculate residue coevolution (coupling scores) between all pairs of residues of a protein.
  The issue is that rather than having a Multiple Sequence Alignment (MSA) which is used as an input by the relevant tools (e.g. evcouplings), I have position wise preferences for 20 amino acids for the protein. </p>
  
  <p>For the protein with length <code>L</code>, I have a <code>20*L</code> matrix of position-wise preferences for amino acids.
  I would like to use this matrix as a direct input for coevolution analysis. </p>
  
  <p>Would it be possible to calculate the residue coevolution direcly from a residue preference matrix?</p>
  
  <p>Any recommendation for a method of choice or a software tool would be helpful.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-05T12:13:30.450Z
Comments.Text: Coevolution requires you to know when you have residue X at position _n_ you will preferentially have Y at _m_. Namely the covariance of _n_ with _m_. If you have a PSSM matrix like you have, you cannot infer the covariance. You would need a `L*L*20*20` tensor.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-05T12:16:56.250Z
Comments.Text: However, your PSSM-like matrix contains useful information, such as what is core and what is surface. But I am not sure what tool uses it. Have a gander at https://predictioncenter.org/casp14/index.cgi
Comments.UserDisplayName: Matteo Ferla
Tags: <proteins><sequence-analysis><mutations>
Title: Residue coevoution from position wise residue preferences rather than multiple sequence alignments
ThreadText: # Residue coevoution from position wise residue preferences rather than multiple sequence alignments
  
  (Asked by: username_0 on 2020-06-05)
  
  Hello experts in residue coevolution analysis of proteins,
  
  I am looking for a way to calculate residue coevolution (coupling scores) between all pairs of residues of a protein.
  The issue is that rather than having a Multiple Sequence Alignment (MSA) which is used as an input by the relevant tools (e.g. evcouplings), I have position wise preferences for 20 amino acids for the protein.
  
  For the protein with length `L`, I have a `20*L` matrix of position-wise preferences for amino acids.
  I would like to use this matrix as a direct input for coevolution analysis.
  
  Would it be possible to calculate the residue coevolution direcly from a residue preference matrix?
  
  Any recommendation for a method of choice or a software tool would be helpful.
  
  **Tags:** proteins, sequence-analysis, mutations
  
  > **Comments:**
  > **username_1**: Coevolution requires you to know when you have residue X at position _n_ you will preferentially have Y at _m_. Namely the covariance of _n_ with _m_. If you have a PSSM matrix like you have, you cannot infer the covariance. You would need a `L*L*20*20` tensor.  
  > **username_1**: However, your PSSM-like matrix contains useful information, such as what is core and what is surface. But I am not sure what tool uses it. Have a gander at https://predictioncenter.org/casp14/index.cgi  
  
  ---
  
  ## 0 answers
  
  