I don't know whether a journal club is one of the purposes of Biostar. But, here goes.
In relation to: http://www.ncbi.nlm.nih.gov/pubmed/19690801
I find the above paper interesting, its using graph theory and statistical approaches to provide functional approximations from the protein sequence.
I really like to know how the formula's work. I could calculate the nearest neighbours but do not have the slightest idea what the formula mean. Got stuck at the 2nd page 2nd column "considering all possible thetha values" and calculating the compactness value Ci and Pi alpha and beta values.
Could you perhaps point to any other resources, that would allow me to understand this further. Or, better break down the actual methods in an intuitive way.
Besides that, I'd like to know any views on this paper - overall limitation, advantages, etc
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I was going to suggest that you discuss the paper at Annotatr, but I guess you already tried this, http://annotatr.appspot.com/citeulike/article/5542986 . Still, please make a question out of this post.
No, BioStar is not a good "journal club" forum. It works best when you have a specific bioinformatics-related query and you suspect that someone has an answer. So as Michael suggested, please try and edit the question to fit those criteria or it will probably be closed.