ProBiS-Database Access
ProBiS-Database is a repository for structurally similar protein binding sites
analysis of the proteins of known structures in the Protein Data Bank (PDB).
Structures of each of the non-redundant PDB entries, currently
42270 of them,
are locally structurally aligned to all other proteins in this database, using ProBiS
local structural alignment algorithm. Non-redundancy to > 95% sequence identical structures
ensures that all the structural variability in the PDB is thoroughly covered. The structural similarity scores of each amino
acid position in the alignment is calculated.
The ProBiS-Database Widget
The ProBiS-Database Widget provides access to the local structural similarity profile for a protein chain.
You can try the fully functioning example below!
Widget:
Usage:
To embed in your own website, copy/paste the following line to your HTML code.
<script type="text/javascript" src="http://probis.cmm.ki.si/pw/?width=150px&title-color=%23faa&body-color=whitesmoke"></script>
Options:
The ProBiS-Database Widget is highly customizable to best fit within your site.
There are a number of options you specify to customize the widget. You can omit
any of these options, and the widget will use default values.
-
width - Specify the width of the widget (ex. 150px). The default width is 280px.
-
title-color - Specify the color of the title and borders in html hex form (ex. #faa). The default is orange.
-
body-color - Specify the color of the body in html hex form (ex. whitesmoke). The default is whitesmoke.
The ProBiS-Database RESTful Web Service Interface
The ProBiS-Database features
RESTful (REpresentational State Transfer) Web Services to make our data easily accessible from your scripts.
ProBiS-Database contains data only for non-redundant PDB chains. This means that you have to use representative non-redundant PDB & Chain IDs
as queries (see examples below).
Perl Example Script
use strict;
use LWP::Simple qw( $ua );
# Make a request command (uncomment lines below if you want something else)
my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/get_alignments?structure_id=1all.A&z_score=2.0');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/get_representative?structure_id=1all.A');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/get_beta_marked_PDB?structure_id=1all.A&z_score=2.0');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/get_superimposition?structure_id1=1all.A&structure_id2=3nmd.B&alignment_no=1');
# Decide about the content type you want to get in return (default is XML) (applies to get_alignments and get_representative; other two commands return "text/plain")
$request->header(Accept => "application/json");
#$request->content_type( 'application/xml' );
# Send the HTTP request
my $response = $ua->request( $request );
# Check to see if there is an error
unless( $response->is_success ) {
print "\n Error: ", $response->status_line, "\n";
}
# Output response
print "ProBiS-Database returned:\n", $response->content;