Question: How To Retrieve The Rna Type From A Pdb File?
1
gravatar for Noam N. Kremen
7.2 years ago by
Noam N. Kremen60 wrote:

I have a large collection of PDB files, each containing the structure of a protein in complex with an RNA molecule. I would like to find out (without going by hand through each PDB) the type of the RNA molecule (tRNA, mRNA, rRNA). Is there any program/web service that can help me achieve this?

pdb rna • 2.2k views
ADD COMMENTlink written 7.2 years ago by Noam N. Kremen60
2
gravatar for Neilfws
7.2 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

One way to do this would be to use PDBML XML files, rather than PDB format. These contain the tag PDBx:pdbx_description, which describes each type of molecule in the structure.

For example, if we search the PDB for molecules containing protein + RNA (using the advanced search facility), choose 3J13, download the XML file and:

grep "PDBx:pdbx_description" 3J13.xml

We see (just showing the first 3 lines):

     <PDBx:pdbx_description>16S ribosomal RNA</PDBx:pdbx_description>
     <PDBx:pdbx_description>mRNA</PDBx:pdbx_description>
     <PDBx:pdbx_description>P site tRNA</PDBx:pdbx_description>

You can parse the XML files in the language of your choice (Ruby, Python, Perl...)

ADD COMMENTlink written 7.2 years ago by Neilfws48k

Thanks, that pointed me in the right direction. Filtering on polyribonucleotide PDBX:type is needed first to get the chain id(s) of the RNA(s).

ADD REPLYlink written 7.2 years ago by Noam N. Kremen60

I don't think that description give fully correct details, esp. for old records. So, you should be careful.

ADD REPLYlink written 7.2 years ago by Vladimir Chupakhin520

Well it's only as good as the PDB curators, obviously.

ADD REPLYlink written 7.2 years ago by Neilfws48k

..that are not always correct.

ADD REPLYlink written 7.2 years ago by Vladimir Chupakhin520
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