Answers.Body: <p>The 43 features are listed in the supplementary materials on page 4. For example,</p>
  <pre><code>Feature Type Atoms Involved 
  1 Distance i, i-5 
  2 Distance i, i-4 
  3 Distance i, i-3 
  4 Distance i, i-2  
  ...
  11 Angle i-1, i, i+1 
  12 Dihedral i, i+1, i+2, i+3 
  </code></pre>
  <p>Are some of them; so Feature 11 is the angle between atom(i-1), atom(i), and atom(i+1). Since it says these were calculated for both the C-alphas and pseudo-centers, this gives 2 * 43. Then this is multiplied by three as mentioned in your quoted paragraph.</p>
  <p>These features (measurements, almost) are numbers, not booleans - so I do not think that they use distance cutoffs as such, although the random forest method is presumably learning various cutoffs and encodes those in the structure of the forest.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-17T16:42:34.093Z
Answers.LastActivityDate: 2022-01-17T16:42:34.093Z
Answers.UserDisplayName: gilleain
Body: <p>In the following article:</p>
  <ul>
  <li><a href="https://pubmed.ncbi.nlm.nih.gov/24995959/" rel="nofollow noreferrer">a fast and efficient Cα-based method for accurately assigning protein secondary structure elements</a></li>
  </ul>
  <p>What are the minimum and maximum cutoff distances in this algorithm?</p>
  <p>Also, what does it mean by:</p>
  <blockquote>
  <p><a href="https://i.sstatic.net/CWKAX.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/CWKAX.png" alt="enter image description here" /></a></p>
  </blockquote>
  <p>I.e. where does (2x43)x3 come from?</p>
  
Tags: <proteins><algorithms>
Title: What is the cutoff distance in this algorithm?
ThreadText: # What is the cutoff distance in this algorithm?
  
  (Asked by: username_0 on 2022-01-17)
  
  In the following article:
  
  * [a fast and efficient Cα-based method for accurately assigning protein secondary structure elements](https://pubmed.ncbi.nlm.nih.gov/24995959/)
  
  What are the minimum and maximum cutoff distances in this algorithm?
  
  Also, what does it mean by:
  
  > [![enter image description here](https://i.sstatic.net/CWKAX.png)](https://i.sstatic.net/CWKAX.png)
  
  I.e. where does (2x43)x3 come from?
  
  **Tags:** proteins, algorithms
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-01-17. Score: 3 | Accepted answer
  
  The 43 features are listed in the supplementary materials on page 4. For example,
  
  ```
  Feature Type Atoms Involved 
  1 Distance i, i-5 
  2 Distance i, i-4 
  3 Distance i, i-3 
  4 Distance i, i-2  
  ...
  11 Angle i-1, i, i+1 
  12 Dihedral i, i+1, i+2, i+3 
  
  ```
  
  Are some of them; so Feature 11 is the angle between atom(i-1), atom(i), and atom(i+1). Since it says these were calculated for both the C-alphas and pseudo-centers, this gives 2 \* 43. Then this is multiplied by three as mentioned in your quoted paragraph.
  
  These features (measurements, almost) are numbers, not booleans - so I do not think that they use distance cutoffs as such, although the random forest method is presumably learning various cutoffs and encodes those in the structure of the forest.
  
  
  ---
  
  