<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>

CC BY-SA 4.0
2022-01-17T16:42:34.093Z
2022-01-17T16:42:34.093Z
gilleain
<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>

<proteins><algorithms>
What is the cutoff distance in this algorithm?
# 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

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## 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.


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