[BiO BB] How to download Protein complexes from PDB ?
skhadar at gmail.com
Thu Sep 13 12:01:13 EDT 2007
Thanks for your detailed mail. But here also the problem is I need to either
check/uncheck 200/5800 structures.
Thats quite a boring job. Anyway right I am working around the Advanced
Search page of RCSB.
PS. I enquired about this at info at rcsb.org and Dr. Catherine explained about
the option that u explained.
On 9/12/07, tcan at ceng.metu.edu.tr <tcan at ceng.metu.edu.tr> wrote:
> You may use the "Advanced Search" utility of PDB to get the complexes you
> 1) Click on the Advanced Search link at the top of the PDB web page at
> 2) Click on the "Choose a query type" pull-down option menu and choose
> "Number of Chains" under "Sequence Features". Specify chain length as:
> between 2 and 4
> 3) Click on the "plus" button on the right to add another sub query
> 4) Click on the second "Choose a query type" pull-down option menu and
> choose "Molecule/Chain Type" under "Structure Summary". Specify "Contains
> Protein: Yes", "Contains DNA: No", and "Contains RNA: No".
> 5) If you want to remove redundant sequences check the "remove similar
> sequences at 90% identity" check-box.
> 6) Click on the "Evaluate Query" button to get the structures you are
> looking for.
> There are about 6K of such complexes. Good luck.
> Tolga Can
> > This is a simple yet a tricky issue : :)
> > I need to download a set of 200 complexes from PDB (they can include
> > dimers, trimers and tetramers). But they should only contain
> > proteins(no
> > DNA/RNA along with the protein). Is it possible get such 200
> > structures from PDB through web search. If yes, what search
> > keyword/strategy should I
> > use ? Or is there any other way to get it done using SRS/BioMart ?
> > SK
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