[BiO BB] Gene ontology PDB files

DGW dgw106 at york.ac.uk
Thu Nov 16 08:34:39 EST 2006


You can search/browse the PDB by GO term from this URL 
http://www.rcsb.org/pdb/static.do?p=search/index.html. You may need to 
have popups enabled on your browser. For example, I can click on Browse 
Database then Molecular Function and I get a tree of function categories 
on the right that I can expand by clicking on the arrows. Following 
'binding' then 'nucleic acid binding', I click on RNA binding (GO 
ID:3723) and get 537 structures. The PDB IDs can be pulled out by using 
the options under Tabulate.

You may need to know the hierarchy of the GO terms you are interested, 
e.g. from AmiGO, as it doesn't appear to be easy to search directly for 
the term of interest at the PDB site. Also, you are not guaranteed to 
find everything of interest - I think the PDB only considers a subset of 
all the available GO terms and even then not all PDB entries have GO 
terms assigned to them. If you need to be more comprehensive you might 
have to BLAST all your gene products against the PDB.

Hope this helps!

Ulisses Dias wrote:
> Hi!
>    Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term?
> Thank you
>   Ulisses Dias
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