Re: [modeller_usage] [clustering] does MODELLER provide tools to cluster structures ?

[Benjamin SCHWARZ <>]

Hi Min-yi Shen, and thanks for sharing your experience,

   As a matter of facts, I was considering the possibility to use such a scheme as the one you describe (RMSD +  linkage ). I didn't realize there could be a symmetry problem with the RMSD distance, but I guess guiding this computation with the multiple alignment should leverage the issue.

    --Ben

Le 24 oct. 2011 à 19:38, Min-yi Shen a écrit :

> My own workaround long time ago (2005) was
> (1) generate N models
> (2) filter out some bad models with objective values
> (3) compute all-against-all RMSDs as a N-by-N matrix (just write a
> double loop in py)
> (4) Do hierarchical agglomerative clustering in R.
> 
> The problem with (4) is that 1. the distance measure from step 3 may
> or may not obey the triangular inequality, and 2. it varies with
> cluster linkage methods.
> 
> so, I finally opted to use some graph-based clustering methods like
> MCL http://micans.org/mcl.