Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-24T21:01:02.290Z
Comments.Text: 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).
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-27T16:52:32.780Z
Comments.Text: Note OP has edited the question.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-29T09:36:05.120Z
Comments.Text: What does accuracy mean in this context? Comparison to human assignment? 53% for DSSP seems low to me.
Comments.UserDisplayName: jgreener
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-29T12:35:09.060Z
Comments.Text: @jgreener, The Q3 (Q8) accuracy is defined as the percentage of residues for which the predicted secondary structures are correct.
Comments.UserDisplayName: user366312
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-29T13:30:35.400Z
Comments.Text: 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.
Comments.UserDisplayName: jgreener
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-29T15:13:08.690Z
Comments.Text: @jgreener, then make some correction in the OP, and post an answer.
Comments.UserDisplayName: user366312
Tags: <proteins><secondary-structure>
Title: Why are DSSP and STRIDE considered reference algorithms, and why do people continue to use them?
ThreadText: # 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**: @username_3, 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**: @username_3, then make some correction in the OP, and post an answer.  
  
  ---
  
  ## 0 answers
  
  