[BioPython] Spatial clustering

[Iddo Friedberg]

Shi-Hsien,


I haven't read the paper you pointed to (yet) but here is a little 
inventory work regarding macine Learning tools that we got:

NaiveBayes, SVM, kMeans, MaxEntropy ... any of those good?

Off biopython, ever considered cluto?

http://www-users.cs.umn.edu/~karypis/cluto/

Best,

Iddo



Shu-Hsien Sheu wrote:
> Hi,
> 
> I am now working on a mapping protein binding site project which would 
> generate thousands of small organic molecules in cartesian coordinates. 
> Next step would be to cluster these small molecules. Is there any 
> modules available for this kind of task? PyCluster seems to work with 2D 
> gene expression data only, thoug through some modifications I can use it 
> as well. I am thinking of using RMSD matrix and then a density-based 
> algorithym. The following paper gave me some general ideas about the 
> approaches I can take:
> 
> http://prlab.ee.memphis.edu/frigui/CLUSTER_PAPERS/Ericasurvey.pdf
> 
> Any comments here?
> 
> thanks!
> 
> -shuhsien
> 
> 
> 
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-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
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