<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>

CC BY-SA 4.0
2020-06-05T12:13:30.450Z
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.
Matteo Ferla
CC BY-SA 4.0
2020-06-05T12:16:56.250Z
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
Matteo Ferla
<proteins><sequence-analysis><mutations>
Residue coevoution from position wise residue preferences rather than multiple sequence alignments
# 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  

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## 0 answers

