Protein-Dna Complexes From Pdb

Question

[AJ]

Hello,

Im trying to 1) get a dataset which has all the protein-DNA bound complexes in PDB. 2) Also, PDB should have the protein and DNA present in the complexes as separate entities also.
How can i go about getting 1 and checking for 2? Thanks everybody.

Cheers, Anj.

Answer 1

[Pierre Poulain]

For 1/ you can list all protein-DNA complexes in the PDB by using the "Advanced search" feature (http://www.pdb.org/pdb/search/advSearch.do) then "Choose a Query Type" -> "Macromolecule Type" and then add as many filters as you want.

For 1/ and 2/, some protein-DNA docking benchmarcks already exist with the partners in their unbound form. See for instance http://haddock.chem.uu.nl/dna/benchmark.html

Answer 2

[Reyhaneh]

1) http://floresta.eead.csic.es/3dfootprint/ can help which is updated weekly using PDB structures. Download at: http://floresta.eead.csic.es/3dfootprint/download.html

2) have a look at this: http://www.ncbi.nlm.nih.gov/pubmed/19906708