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closeIsn't this invalidating the method?
Posted by raik on 26 Jun 2010 at 12:48 GMT
Surprisingly, the similarity P-value analysis of these 53 pairs revealed that the physico-chemical similarity of the mimicking binding sites is not significant. However, their structural similarity is obvious, see Figure 2.
http://ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000821#article1.body1.sec3.p5
The cases of obvious structural mimicry are a perfect positive control for the method used in this paper. The fact that what we know is similar is not actually classified as similar puts, in my opinion, a big question mark on this work.
RE: Isn't this invalidating the method?
juliettemartin replied to raik on 28 Jun 2010 at 08:43 GMT
Dear Raik
In this paper, I counted the number of similar atoms/residues at the interface among all the atoms/residues that are structurally aligned. By similar, I meant atoms or residues from the same physico-chemical class.
I would not say that obvious cases of structural mimicry are a perfect positive control, since the similarity between them is structural, i.e., the shape of the binding sites. Shape is not taken into account in the present study.
Juliette Martin