[BiO BB] may I use GO to identify functional similar proteins

[Boris Steipe]

A number of similarity measures on GO have been defined in the  
literature. Once you have a PDB ID, get the corresponding UniProt ID,  
then use FunSimMat to find other proteins of similar function. The  
authors discuss the concepts and pitfalls of such an approach in  
their 2007 NAR paper.

    http://funsimmat.bioinf.mpi-inf.mpg.de/

However this approach does not really operate on independent data: a  
very large number of GO annotations is "inferred from electronic  
annotation" - i.e. more or less from a BLAST search. You are likely  
to get very similar information by simply doing a BLAST (or VAST)  
search in the first place: homologous proteins have similar function.  
But try it, it's quite informative.

HTH,
Boris


On 28-May-08, at 2:37 PM, Xue Li wrote:

> Hello all,
>
> Does anyone know whether I could use GO to identify functional similar
> proteins? Given a protein pdbID, can I search GO for functional
> similar proteins? Thanks.
>
> -- 
> Xue, Li
> Bioinformatics and Computational Biology program @ ISU
> Ames, IA 50010
> 515-450-7183
>
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