Katherine
I am not exactly sure what sort of tool you would like to use, but there are
a couple of options found here...
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/
The last option DB search
http://www.ebi.ac.uk/pdbe-as/pdbesearch/
allows you upload a fragment of structure - a small number of residues
that are arranged in space,
typically an active site. For example, you can upload an example of the
catalytic triad (or quartet)
as a PDB file. You need only provide the atom records for 6 or less
residues cut out of a normal
PDB file from any source. This will search the
entire PDB for this arrangement of residues based on the CA atoms or
side chain atoms; the
latter is slower and can take a minute.
The search will either match residue type exactly with geometry, or
match similar residues (ie acid to acid).
The three other tools from the main page
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/
allow you carry out various analysis of the PDB using a pre calculated
set of residue arrangements
such as the catalytic triad / quartet. These 1972 residue arrangements
(some are active sites) were
generated by statistical data mining using a Bayesian statistical
methods to identify these
residue patterns. You can browse these:
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/DMfragmentsBrowse.jsp
search 1 protein with 1 fragment :
http://www.ebi.ac.uk/pdbe-as/pdbetemplate/DMSingleFit.jsp
or label a single protein with all the 1972 data mined fragments. A
sort of auto-annotation
of a structure with predefined fragments.
You should be aware that the fragment database was calculated using a
mathematical
target which does not say what biological role of the fragments in the
data. They are
provided as a means to carry out your own research.
Tom
I don't know whether your question is specifically for protein-ligand
interactions, protein-protein interactions, internal protein
interactions, etc., but one place to start is to look at some of the
database tools already available on-line, including, for example,
CREDO from Tom Blundell's group, which is a nice database of pairwise
interactions (intra- and intermolecular) between ligands and proteins.
There are also commercial products that do interaction searches in the
PDB, but they are quite expensive.
------------------------------------------------
P. Shing Ho, Ph.D.
Professor & Chair
Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Fort Collins, CO 80523-1870
970-491-0569 (phone)
From: Katherine Sippel <katherine.sip...@gmail.com
<mailto:katherine.sip...@gmail.com>>
Reply-To: Katherine Sippel <katherine.sip...@gmail.com
<mailto:katherine.sip...@gmail.com>>
Date: Monday, October 28, 2013 12:23 PM
To: "CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>"
<CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Data mining interactions in the PDB
Hi all,
I was wondering if anyone knew of a software or server to mine the PDB
for a specific class of interactions? I've tried PDBeMotif without
much luck and I thought I'd check to see if there was an alternative
before I go re-inventing the wheel.
Cheers,
Katherine
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