[BiO BB] How to download Protein complexes from PDB ?

[tcan at ceng.metu.edu.tr]

You may use the "Advanced Search" utility of PDB to get the complexes you
need.

1) Click on the Advanced Search link at the top of the PDB web page at
www.rcsb.org/pdb

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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