Searching the PDB for sequence with structure
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
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 >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | Lab: (406) 994-6237 | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================
Florian Odronitz wrote: > 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_.
Unless I misunderstand your question, this is exactly what we do in step 1 of the basic tutorial at http://salilab.org/modeller/tutorial/basic.html
This uses Modeller's profile.build() method to search a database of sequences, which in this case is every sequence from PDBs with structure, filtered at 95% to remove redundancy. It is not a BLAST search but rigorous dynamic programming.
Ben Webb, Modeller Caretaker
participants (3)
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Florian Odronitz -
Mensur Dlakic -
Modeller Caretaker