What does it mean by PC in this article?

  • Thread starter Thread starter user366312
  • Start date Start date
  • Tags Tags
    article Mean pc
AI Thread Summary
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.
user366312
Gold Member
Messages
88
Reaction score
3
https://pubmed.ncbi.nlm.nih.gov/24995959/

What does it mean by PC in this article?

1642412060817.png
 
Chemistry news on Phys.org
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?
 
I want to test a humidity sensor with one or more saturated salt solutions. The table salt that I have on hand contains one of two anticaking agents, calcium silicate or sodium aluminosilicate. Will the presence of either of these additives (or iodine for that matter) significantly affect the equilibrium humidity? I searched and all the how-to-do-it guides did not address this question. One research paper I found reported that at 1.5% w/w calcium silicate increased the deliquescent point by...
I was introduced to the Octet Rule recently and make me wonder, why does 8 valence electrons or a full p orbital always make an element inert? What is so special with a full p orbital? Like take Calcium for an example, its outer orbital is filled but its only the s orbital thats filled so its still reactive not so much as the Alkaline metals but still pretty reactive. Can someone explain it to me? Thanks!!
I'm trying to find a cheap DIY method to etch holes of various shapes through 0.3mm Aluminium sheet using 5-10% Sodium Hydroxide. The idea is to apply a resist to the Aluminium then selectively ablate it off using a diode laser cutter and then dissolve away the Aluminium using Sodium Hydroxide. By cheap I mean resists costing say £20 in small quantities. The Internet has suggested various resists to try including... Enamel paint (only survived seconds in the NaOH!) Acrylic paint (only...
Back
Top