Re: [modeller_usage] Searching the PDB for sequence with structure
To: Florian Odronitz <>
Subject: Re: [modeller_usage] Searching the PDB for sequence with structure
From: Modeller Caretaker <>
Date: Wed, 28 May 2008 11:08:34 -0700
Cc:
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_.
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.