question_about_GPCR paper

[karolk]

Hi Xinqiu,

(1) I would have a question, regarding the paper about GPCR (Yao et al. 2015).

In Figure 3c you present your network.

Are these after amendments or pure "net" directly after cna()?

(2) Second issue: I could see that sometimes after network amendment (performed using script, which is presented in GDP/GTP tutorial), my network gets destroyed. Important edges disappear, the size of my communities does not correspond to this what I would expect from my system, and sometimes the communities are simply moved outside of a protein May I ask what may cause this problem? I mean, how the exact location of community is determined? Is its position averaged based on xyz of all residues, which belong to each community or something in this spirit?

Another question: does it pay off to coarse grain network even more, if modularity of my net after CNA looks reasonable.? True, part of the protein after amendment looks better, but another part looks a bit unrealistic.

thanks

[Xinqiu Yao]

Hi,

For question (1), do you mean the JBC 2016 paper? Figure 3c in that paper is after an adjustment of number of communities based on modularity (so-called "amendment"), along with a fine-tuning of community boundaries based on network analysis results of all nucleotide states, secondary structure definitions, and prior knowledge about the system (e.g. known motifs for nucleotide binding). The results represent a consensus community partitioning for all states (See the paper for detail).

(2) How exactly did you implement the script for amendment? Could you provide with a more specific example with both input (commands and data) and output (figures, etc.), and explain what are unexpected?

Low modularities normally indicate bad partitions but if values are near optimal, I would say the quality of partitions are comparable. So, yes, you could get pay off by leveling up the coarse graining. It always depends on systems. Provide with a more specific example and then we can discuss in more detail.

[Barry Grant]

This is not an "issue" related to the code base of Bio3D. Please don't post as a "bug" here but perhaps as a Q&A or even in a different forum. Thanks!