Question: How to get PDB ID from sequence accession number ?
0
gravatar for Mahmoud Ahmed
3.1 years ago by
Egypt,Cairo
Mahmoud Ahmed0 wrote:

I have a list of protein accession ids and if it is a known protein
I would like to have the corresponding links to PDB.(i.e corresponding PDB codes)
How can I get the PDB codes if I have the GenBank protein accession ids to make software can do this operation automatically?

Example:
Having the accession number CAD66663 ,I would like to have PDB code for this. 

 

blast protein ncbi pdb • 3.4k views
ADD COMMENTlink modified 3.1 years ago by Elisabeth Gasteiger1.6k • written 3.1 years ago by Mahmoud Ahmed0
1

You should be able to use upload a bunch of IDs to NCBI BLAST or use standalone blast+ to query against pdb. Some filtration should get you the PDB ids.

ADD REPLYlink written 3.1 years ago by RamRS20k
0
gravatar for Elisabeth Gasteiger
3.1 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

If you are doing this programmatically, you could try going via UniProtKB, and use URLs of the form

http://www.uniprot.org/uniprot/?query=database%3A%28type%3Aembl%20CAD66663%29&format=tab&columns=id%2Cdatabase%28PDB%29

In this particular case, there is no PDB cross-reference in UniProtKB, but here is a case where there is:

http://www.uniprot.org/uniprot/?query=CAA26306&sort=score&format=tab&columns=id%2Cdatabase%28PDB%29

ADD COMMENTlink written 3.1 years ago by Elisabeth Gasteiger1.6k
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