<p>Hey i solve this simply by use of SOV alghoritm. <a href="https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment" rel="nofollow noreferrer">https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment</a></p>

<p>cheers</p>

CC BY-SA 4.0
2020-04-01T15:48:18.407Z
2020-04-01T15:48:18.407Z
MTG
<p>I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well.</p>

<p>Example:</p>

<pre><code>EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC

EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCEEEEEEEEEEEEEE
</code></pre>

<p>Example of matching:</p>

<pre><code>EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
|||        |||||| |||                    |||||||||     ||||||      |   |||    ||
EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHEEEECCCCCCCCCCEEEEEEEEEE
</code></pre>

<p>Hypothetically: 50% aligned - > score 0.5 - >  thats scoring is wrong:</p>

<pre><code>EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
||||||||||||||||||||||||||||||||||||||||||
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH
</code></pre>

<p>This case will have similar score... </p>

<p>This is a puzzle for me, I don't know how to approach it technically.</p>

CC BY-SA 4.0
2019-12-15T21:49:30.900Z
Normally 3D structures of protein are compared and the RSMD is reported. How did you get your SS, with JPred or from PDBs? Comparing SS might result in some biases: if one of the two protein is getting used as a template for the other say or if both are from PDBs but the SS was called different (if so, use DSS on both). Also note that JPred is like 75% accurate at best.
Matteo Ferla
CC BY-SA 4.0
2019-12-16T10:02:56.217Z
@MatteoFerla I suspect that these are predicted secondary structures.
James
CC BY-SA 4.0
2019-12-16T10:15:51.810Z
@James Exactly my worry (I see a helix of a single AA in a coil). The solution is straightforward, but I am not sure how one could add error estimates to said solutions, which seems like a must...
Matteo Ferla
CC BY-SA 4.0
2019-12-16T10:20:34.043Z
I suppose using data from JPred, PSIPRED, SPIDER2 and doing the 9 pairwise alignments would suffice on a push.
Matteo Ferla
CC BY-SA 4.0
2019-12-16T10:28:18.520Z
@MatteoFerla I agree. In lieu of a structure, usually, a meta-prediction would suffice. I think MTG should add why the sequences are being aligned. I think different tools should be used depending on if they are checking to see how much secondary structure prediction error is in a sequence compared to a reference sequence, or if they are checking secondary structure as a proxy for structural divergence.
James
CC BY-SA 4.0
2019-12-16T17:38:39.417Z
It is a predicted SS with GOR method. I try to add sorting by SS to my algorihtm. First version will use garnier (emboss) method. Sequences are aligned because program align similar sequences. Then I add SS to check aligned proteins (additional validation). I plan to use spider or jpred in future.
MTG
CC BY-SA 4.0
2019-12-17T00:34:58.127Z
In summary, this is a very provisional analysis, providing a starting point to further de novo prediction methods. We all assume the crystal structures are not present here
M__
<proteins><python><r><secondary-structure>
protein secondary structure matching/comparison scoring
# protein secondary structure matching/comparison scoring

(Asked by: username_0 on 2019-12-15)

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well.
Example:
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC

EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCEEEEEEEEEEEEEE

Example of matching:
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
|||        |||||| |||                    |||||||||     ||||||      |   |||    ||
EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHEEEECCCCCCCCCCEEEEEEEEEE

Hypothetically: 50% aligned - > score 0.5 - >  thats scoring is wrong:
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
||||||||||||||||||||||||||||||||||||||||||
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH

This case will have similar score... 
This is a puzzle for me, I don't know how to approach it technically.

**Tags:** proteins, python, r, secondary-structure
> **Comments:**
> **username_1**: Normally 3D structures of protein are compared and the RSMD is reported. How did you get your SS, with JPred or from PDBs? Comparing SS might result in some biases: if one of the two protein is getting used as a template for the other say or if both are from PDBs but the SS was called different (if so, use DSS on both). Also note that JPred is like 75% accurate at best.  
> **username_2**: @MatteoFerla I suspect that these are predicted secondary structures.  
> **username_1**: @James Exactly my worry (I see a helix of a single AA in a coil). The solution is straightforward, but I am not sure how one could add error estimates to said solutions, which seems like a must...  
> **username_1**: I suppose using data from JPred, PSIPRED, SPIDER2 and doing the 9 pairwise alignments would suffice on a push.  
> **username_2**: @MatteoFerla I agree. In lieu of a structure, usually, a meta-prediction would suffice. I think MTG should add why the sequences are being aligned. I think different tools should be used depending on if they are checking to see how much secondary structure prediction error is in a sequence compared to a reference sequence, or if they are checking secondary structure as a proxy for structural divergence.  
> **username_0**: It is a predicted SS with GOR method. I try to add sorting by SS to my algorihtm. First version will use garnier (emboss) method. Sequences are aligned because program align similar sequences. Then I add SS to check aligned proteins (additional validation). I plan to use spider or jpred in future.  
> **username_3**: In summary, this is a very provisional analysis, providing a starting point to further de novo prediction methods. We all assume the crystal structures are not present here  

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## 1 answers

### Answer by username_0 on 2020-04-01. Score: 1 | Accepted answer

Hey i solve this simply by use of SOV alghoritm. <https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment>

cheers


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