Question: Gene Ontology Terms For A Set Of Pdb Chains
0
gravatar for Reyhaneh
7.7 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

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.

gene pdb • 1.8k views
ADD COMMENTlink written 7.7 years ago by Reyhaneh480
2
gravatar for Rachael
7.7 years ago by
Rachael20
Rachael20 wrote:

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.

ADD COMMENTlink written 7.7 years ago by Rachael20

Thanks. It really helped.

ADD REPLYlink written 7.7 years ago by Reyhaneh480
0
gravatar for Chris Penkett
7.7 years ago by
Chris Penkett480
Cambridge, UK
Chris Penkett480 wrote:

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

http://biostar.stackexchange.com/questions/6164/different-protein-go-annotation-results-depending-on-their-source-uniprot-amigo

Chris

ADD COMMENTlink written 7.7 years ago by Chris Penkett480
0
gravatar for Chris
7.7 years ago by
Chris1.6k
Munich
Chris1.6k wrote:

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.
ADD COMMENTlink written 7.7 years ago by Chris1.6k
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