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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