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

[Modeller Caretaker <modeller-care@ucsf.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
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