What does it mean by PC in this article?

[user366312]

https://pubmed.ncbi.nlm.nih.gov/24995959/

What does it mean by PC in this article?

 

[Melbourne Guy]

From the paper, PC is pseudo-center, @user366312.

Specifically, they are referring to the application: "SABA uses a similar approach to P-SEA but instead of directly computing the Cα coordinates SABA shifts the coordinates of the ith Cα atom to its pseudo-center (PC) position (defined as the center-of-geometry between Cα(i) and Cα(i+1)) and then assigns SSEs based on an optimized set of PC-dependent geometric criteria. This is thought to better represent the location of the backbone N-H/C=O atoms involved in secondary structure formation."

The application in the paper, PCASSO (Protein C-Alpha Secondary Structure Output), is an alternative approach to SABA (and others) that claims to be fast and efficient in assigning protein SSEs that only requires Cα atoms as input.

 

[user366312]

I see that the minimum cut-off distance is 6.
What is the maximum cut-off distance?

 

[Melbourne Guy]

I see that the minimum cut-off distance is 6.
What is the maximum cut-off distance?

Are you referring to the k^th residue as 'distance'? If so, can't see a maximum, it is probably an accuracy function rather than a specific value.

 

[user366312]

What does it actually mean by a "cut-off" in this PCASSO algorithm?

 

[Melbourne Guy]

What does it actually mean by a "cut-off" in this PCASSO algorithm?

Can you note the section of the paper where you're reading this, @user366312, because I am not sure what aspect of PCASSO you are referring to?