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

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.

Gold Member
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 kth residue as 'distance'? If so, can't see a maximum, it is probably an accuracy function rather than a specific value.

Gold Member
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?