Gene Ontology Terms For A Set Of Pdb Chains

Question

[Reyhaneh]

Hi;

I have a set of PDBCodes-chain such as 1AFV-A, 1AFV-M, 2RMA-A,... and for each chain I would like to find the corresponding GO term.How Can I do this?

I have noticed that using RCSBPDB with the following URL you can have the GO terms:

such as: http://www.pdb.org/pdb/rest/goTerms?structureId=2kri.A

I have tried using gene ontology website as well: http://www.geneontology.org/

But it is strange since for 1AFV-A RCSBPDB I (http://www.pdb.org/pdb/rest/goTerms?structureId=1afv) will get no results while gene ontology website gives one result.

Can you please tell me how can I deal with finding the GO terms?

Thanks in advance.

Answer 1

[Rachael]

Hi Reyhaneh,

You can download the Gene Association File for PDB from the UniProt-GOA website here; http://www.ebi.ac.uk/GOA/downloads.html just scroll down to the PDB Gene Association link in the table. The file format is described in the Readme found in the same folder.

Rachael.

[Reyhaneh]

Thanks. It really helped.

Answer 2

[Chris Penkett]

There is a related post here about different databases having varying numbers of GO terms.

Chris

Answer 3

[Chris]

You may want to take a look into SwissProt. They have crossreferences to PDB and GO. Look for lines in one entry such as

DR   PDB; 2E9Q; X-ray; 2.20 A; A=22-480.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.