Subject: Re[2]: PDB 3D queries?

From: [email-masked] (BRYAN MARTEN)
Date: Mon, 27 Jul 1998 11:40:16 -0400

Thanks to several people for pointing me to IsoStar for doing 3D searches of the
PDB.  I am interested in alternatives to IsoStar, though.  I have yet to use
IsoStar, but from its web page's FAQ (http://www.ccdc.cam.ac.uk/isostar/
faq.html) I see that there are some potentially significant limitations,
particularly if you are interested in general amino acid-amino acid interactions
or oddball queries.  With IsoStar, all interactions internal to proteins are
excluded from the database (see FAQ excerpt below).  Also, the types of queries
which can be made are limited (see other FAQ excerpt below).

Bryan Marten
[email-masked]

Excerpted from IsoStar FAQ:

Exactly which contacts does IsoStar include from the PDB?

First, we don't include contacts between protein atoms - only between protein
atoms and ligand atoms, protein atoms and water, and ligand atoms and water.
Secondly, we only use PDB structures with a resolution better than 2.5A.
Thirdly, when there is a "family" of PDB structures which are identical except
for one or more mutated residues in the protein, we only use one of them.
Fourthly, we have excluded covalently-bound protein-ligand complexes. Finally,
some structures were excluded because we couldn't process them correctly or were
unsure of the ligand structure.

Why are there no results for some central-group/contact-group combinations in
IsoStar, when I'm sure there are structures in the databases that contain them?

Two possible reasons. First, we just may not have done the search yet. It takes
quite a long time to do them all. Secondly, we don't use all PDB structures -
for example, low resolution structures (poorer than 2.5A) are excluded.