What does it mean by PC in this article?

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In the discussed article, "PC" stands for pseudo-center, which is used in the context of the PCASSO (Protein C-Alpha Secondary Structure Output) application. This method shifts the coordinates of Cα atoms to their pseudo-center position, defined as the center-of-geometry between consecutive Cα atoms. This adjustment aims to enhance the accuracy of secondary structure element (SSE) assignments by better representing the locations of backbone N-H/C=O atoms involved in secondary structure formation. The paper mentions a minimum cut-off distance of 6, but the maximum cut-off distance is not specified, suggesting it may relate more to accuracy rather than a defined value. The term "cut-off" in the PCASSO algorithm likely refers to a threshold used in the analysis, although further clarification from specific sections of the paper is needed for a more precise understanding.
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https://pubmed.ncbi.nlm.nih.gov/24995959/

What does it mean by PC in this article?

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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.
 
I see that the minimum cut-off distance is 6.
What is the maximum cut-off distance?
 
user366312 said:
I see that the minimum cut-off distance is 6.
What is the maximum cut-off distance?
Are you referring to the kth residue as 'distance'? If so, can't see a maximum, it is probably an accuracy function rather than a specific value.
 
What does it actually mean by a "cut-off" in this PCASSO algorithm?
 
user366312 said:
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?
 
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