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

[Mensur Dlakic <mdlakic AT montana.edu>]

Try Dunbrack's lab page, specifically S2C:

http://dunbrack.fccc.edu/Guoli/s2c/index.php

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

http://astral.berkeley.edu/scopseq-1.73.html


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,
> Florian
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