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

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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