[modeller_usage] Searching the PDB for sequence with structure

[Florian Odronitz <>]

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,
Florian