<p>I am working on globular protein secondary structure assignments. The purpose of my project is to design an improved algorithm for secondary structure assignment.</p>
<p>I know two tools: <code>DSSP</code> and <code>STRIDE</code> for secondary structure prediction and assignment.</p>
<p>However, their accuracy [the Q3 (Q8) accuracy is defined as the percentage of residues for which the predicted secondary structures are correct] is around 53% and 70%, respectively, which isn't much if we compare them to modern algorithms like <code>PALSSE</code>, etc.</p>
<p>If so, why are <code>DSSP</code> and <code>STRIDE</code> considered reference algorithms, and why do people continue to use them?</p>

CC BY-SA 4.0
2024-04-24T21:01:02.290Z
This question is not specific enough. Please add more context to your post to describe a specific bioinformatics problem. Generic "What's the best tool" questions are better asked in discussion-type places like [Reddit](https://reddit.com/r/bioinformatics).
gringer
CC BY-SA 4.0
2024-04-27T16:52:32.780Z
Note OP has edited the question.
M__
CC BY-SA 4.0
2024-04-29T09:36:05.120Z
What does accuracy mean in this context? Comparison to human assignment? 53% for DSSP seems low to me.
jgreener
CC BY-SA 4.0
2024-04-29T12:35:09.060Z
@jgreener, The Q3 (Q8) accuracy is defined as the percentage of residues for which the predicted secondary structures are correct.
user366312
CC BY-SA 4.0
2024-04-29T13:30:35.400Z
But what is the source of ground truth? DSSP and STRIDE assign secondary structure from tertiary structure rather than predict it from sequence. I see the number 53% for DSSP in the PALSSE paper, but that is not for Q3 or Q8 accuracy.
jgreener
CC BY-SA 4.0
2024-04-29T15:13:08.690Z
@jgreener, then make some correction in the OP, and post an answer.
user366312
<proteins><secondary-structure>
Why are DSSP and STRIDE considered reference algorithms, and why do people continue to use them?
# Why are DSSP and STRIDE considered reference algorithms, and why do people continue to use them?

(Asked by: username_0 on 2024-04-23)

I am working on globular protein secondary structure assignments. The purpose of my project is to design an improved algorithm for secondary structure assignment.

I know two tools: `DSSP` and `STRIDE` for secondary structure prediction and assignment.

However, their accuracy [the Q3 (Q8) accuracy is defined as the percentage of residues for which the predicted secondary structures are correct] is around 53% and 70%, respectively, which isn't much if we compare them to modern algorithms like `PALSSE`, etc.

If so, why are `DSSP` and `STRIDE` considered reference algorithms, and why do people continue to use them?

**Tags:** proteins, secondary-structure
> **Comments:**
> **username_1**: This question is not specific enough. Please add more context to your post to describe a specific bioinformatics problem. Generic "What's the best tool" questions are better asked in discussion-type places like [Reddit](https://reddit.com/r/bioinformatics).  
> **username_2**: Note OP has edited the question.  
> **username_3**: What does accuracy mean in this context? Comparison to human assignment? 53% for DSSP seems low to me.  
> **username_0**: @jgreener, The Q3 (Q8) accuracy is defined as the percentage of residues for which the predicted secondary structures are correct.  
> **username_3**: But what is the source of ground truth? DSSP and STRIDE assign secondary structure from tertiary structure rather than predict it from sequence. I see the number 53% for DSSP in the PALSSE paper, but that is not for Q3 or Q8 accuracy.  
> **username_0**: @jgreener, then make some correction in the OP, and post an answer.  

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## 0 answers

