Answers.Body: <p><em>Answer from @jan-wilamowski, converted from comment:</em></p>
  <p>That second paper seems to distinguish between the known data that is used for ML training (i.e. amino acid sequences are assigned some secondary structure) and the attempt to replicate this natural assignment by an &quot;artificial&quot; prediction.</p>
  
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Answers.UserDisplayName: gringer
Answers.Body: <p>To make it crystal clear (and make than pun):</p>
  <ul>
  <li><code>Assignment</code>: a 3D structure is known and the residues are <em>assigned</em> a secondary structure</li>
  <li><code>Prediction</code>: an algorithm predicts from linear (primary) sequence what the secondary structure may be —often incorrectly. This can be homology based, covariance, deep learning etc. But most commonly just the vector norm of window residue composition, e.g. proline is never in a helix and helices and sheets have different periodicity (two for a sheet and three and a bit for a helix).</li>
  </ul>
  
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Answers.Text: What do you mean by *3D structure*? Is it a Secondary or Tertiary structure?
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Answers.Text: Tertiary/quaternary structure —which may be of only part of the protein and with gaps due to technical limitations. But I mean specifically a list of atomic coordinates (eg. [PDB file](https://en.m.wikipedia.org/wiki/Protein_Data_Bank_(file_format) )) of that chain, possibly as an oligomer, with a ligands or other chains as opposed to say just the name of the fold, e.g. Rossmann fold.
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Answers.UserDisplayName: Matteo Ferla
Body: <p>I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML.</p>
  <p>When it comes to protein analysis, most of the books or research papers talk about protein structure <strong>Prediction</strong>:</p>
  <p><a href="https://bip.weizmann.ac.il/course/structbioinfo/pdf/SecondaryStructurePrediction_WIS.pdf" rel="nofollow noreferrer">https://bip.weizmann.ac.il/course/structbioinfo/pdf/SecondaryStructurePrediction_WIS.pdf</a></p>
  <p>Only a handful of books or articles talk about protein structure <strong>Assignments</strong>:</p>
  <p><a href="https://www.biorxiv.org/content/10.1101/2021.02.02.429329v1" rel="nofollow noreferrer">https://www.biorxiv.org/content/10.1101/2021.02.02.429329v1</a></p>
  <p>Can anyone tell me what is the basic difference between Assignment and Prediction?</p>
  <p>Kindly explain with examples.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-05T05:40:04.263Z
Comments.Text: Do you have any examples for the use of Protein Structure Assignment? [This paper](https://pubmed.ncbi.nlm.nih.gov/8749853/) uses the term in the title but they don't particularly distinguish the terminology.
Comments.UserDisplayName: Jan Wilamowski
Tags: <proteins><protein-structure><secondary-structure>
Title: What is protein secondary structure assignment?
ThreadText: # What is protein secondary structure assignment?
  
  (Asked by: username_0 on 2021-07-05)
  
  I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML.
  
  When it comes to protein analysis, most of the books or research papers talk about protein structure **Prediction**:
  
  <https://bip.weizmann.ac.il/course/structbioinfo/pdf/SecondaryStructurePrediction_WIS.pdf>
  
  Only a handful of books or articles talk about protein structure **Assignments**:
  
  <https://www.biorxiv.org/content/10.1101/2021.02.02.429329v1>
  
  Can anyone tell me what is the basic difference between Assignment and Prediction?
  
  Kindly explain with examples.
  
  **Tags:** proteins, protein-structure, secondary-structure
  
  > **Comments:**
  > **username_1**: Do you have any examples for the use of Protein Structure Assignment? [This paper](https://pubmed.ncbi.nlm.nih.gov/8749853/) uses the term in the title but they don't particularly distinguish the terminology.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2021-07-05. Score: 7 | Accepted answer
  
  To make it crystal clear (and make than pun):
  
  * `Assignment`: a 3D structure is known and the residues are *assigned* a secondary structure
  * `Prediction`: an algorithm predicts from linear (primary) sequence what the secondary structure may be —often incorrectly. This can be homology based, covariance, deep learning etc. But most commonly just the vector norm of window residue composition, e.g. proline is never in a helix and helices and sheets have different periodicity (two for a sheet and three and a bit for a helix).
  
  > **Comments:**
  > **username_0**: What do you mean by *3D structure*? Is it a Secondary or Tertiary structure?  
  > **username_3**: Tertiary/quaternary structure —which may be of only part of the protein and with gaps due to technical limitations. But I mean specifically a list of atomic coordinates (eg. [PDB file](https://en.m.wikipedia.org/wiki/Protein_Data_Bank_(file_format) )) of that chain, possibly as an oligomer, with a ligands or other chains as opposed to say just the name of the fold, e.g. Rossmann fold.  
  
  ---
  
  ### Answer by username_2 on 2021-07-05. Score: 1
  
  *Answer from @jan-username_1, converted from comment:*
  
  That second paper seems to distinguish between the known data that is used for ML training (i.e. amino acid sequences are assigned some secondary structure) and the attempt to replicate this natural assignment by an "artificial" prediction.
  
  
  ---
  
  