The ProBiS-Database WidgetThe ProBiS-Database Widget provides access to the local structural similarity profile for a protein chain. You can try the fully functioning example below! |
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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>
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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.
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The ProBiS-Database RESTful Web Service InterfaceThe 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). |
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Get RepresentativeTranslate your PDB & Chain ID to > 95% sequence identical representative: /rest/get_representative?structure_id=1ytf.A |
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Get Local Structural AlignmentsGet local structural alignments with Z-Scores>2.0 for a representative: /rest/get_alignments?structure_id=1ytb.B&z_score=2.0 |
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Get SuperimpositionGet the PDB file of two superimposed representative structures: /rest/get_superimposition?structure_id1=1all.A&structure_id2=3nmd.B&alignment_no=1 |
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Get Similarity ScoresGet representative with similarity scores in beta-factors at Z-Score>2.0: /rest/get_beta_marked_PDB?structure_id=1all.A&z_score=2.0 |
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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; |