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Re: [modeller_usage] Searching the PDB for sequence with structure

Try Dunbrack's lab page, specifically S2C:


ASTRAL also offers ATOM-based database of sequences, but unfortunately only for PDB entries present in SCOP (lags a year or two behind PDB):


At 02:33 AM 5/28/2008, Florian Odronitz wrote:
Hi Modelleros,

I am in the process of modeling ~100 similar structures. I have a
bunch of templates that cover most of the sequence of the targets.
However, there are some gaps. Most gaps are loop regions or contain
loops, sometimes comprising ~30 aas, so ab initio modeling is not an
option. So I go to the PDB and BLAST with my missing sequence as a
query. I get a great number of hits but for most of the PDBs, the
large parts of the sequence have no _structure_. Downloading each of
those PDBs and looking at them is not an option since its hundreds.
I am looking for a tool to BLAST (or otherwise search) the sequences
in the PDB that have _structure_. The people at the PDB told me there
is no such option and they are not aware of such an  resource.
I figure I am not the first person to encounter such a difficulty. How
would you handle this? Is there such a resource?

Thanks and best regards,
modeller_usage mailing list


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