See also: http://www.geneontology.org/GO.tools.shtml
The developers of many of these tools hang out on the gofriends list, you may want to ask there too: [EMAIL PROTECTED] On May 28, 2008, at 12:32 PM, Boris Steipe wrote: > 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 >> >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
