[BiO BB] Gene ontology PDB files
ulimard at yahoo.com.br
Sat Nov 18 17:24:45 EST 2006
Thank you so much for your reply. However I have a doubt using the browse and download csv tools.
For example, I've clicked on Browse Database then Molecular Function and I get a tree of functions categories on the right that I can expand by clicking on the arrows. Following 'binding' then 'nucleic acid binding', I click on 'DNA binding (Go
ID: 3677) and the first PDB ID that I get is the '10MH', but when I use the 'Custom Report' tool this structure id appears with the GO ID = 'n/a'. This kind of problem happens with some others structures.
Please, tell me if I'm trying something wrong.
Once again, thank you so much!
DGW <dgw106 at york.ac.uk> escreveu: Hi,
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:
> Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term?
> Thank you
> Ulisses Dias
> Fale com seus amigos de graça com o novo Yahoo! Messenger
> General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu celular. Registre seu aparelho agora!
More information about the BBB