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Introduction
  • There are two ProBiS web pages out there: ProBiS at http://probis.cmm.ki.si maintained at the National Institute of Chemistry, Slovenia, and ProBiS-CHARMMing at http://probis.nih.gov situated at the National Institutes of Health, USA. Why is that? ProBiS-CHARMMing has additional functions only available from inside NIH: it enables energy minimization of predicted protein-ligand complexes and their interaction energy calculation.
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ProBiS-Web Server RESTful Web Services

The ProBiS-Web Server features RESTful (REpresentational State Transfer) Web Services to make the binding site similarities and local pairwise alignments for any PDB protein structure easily accessible from your scripts. Full set of commands and useful examples are listed below.

Pairwise Alignment of PDB Structures

Examples:

Specification:

  • structure_id1, structure_id2 - Specifies the PDB/Chain ID(s) of PDB structures to compare (ex. 1all.A, 3dbj.C). For two chains use 1all.AB, 3dbj.CD.
  • bsite1, bsite2 (optional) - Specifies the binding sites to compare (ex. CYC.175.A.7, CYC.201.C.7). E.g., CYC - ligand name, 175 - ligand number, A - chain id, 7 - radius in Angstroms to select residues around ligand. If omitted, entire PDB structures are aligned.
  • return (optional) - Specifies the return type, which can be pdb, json, or xml. The default is xml.

Detect Similar Proteins or Binding Sites in the Non-redundant PDB

Caution: Examples in this section require all CPUs of the ProBiS-web server, and can load several minutes depending on the server work load.

Examples:

Specification:

  • structure_id - Specifies the PDB/Chain ID(s) of the query PDB structure to be compared with all proteins in the nr-PDB (ex. 5cyt.R).
  • bsite (optional) - Specifies the query binding site to search against nr-PDB (ex. HEM.105.R.5). E.g., HEM - ligand name, 105 - ligand number, R - chain id, 5 - radius in Angstroms to select residues around ligand. If omitted, entire PDB structure is considered as a query.
  • z_score (optional) - Specifies the cutoff Z-Score; alignments with Z-Score>cutoff will be returned. The default is 1.0.
  • return (optional) - Specifies the return type, which can be json or xml. The default is xml.

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/align?structure_id1=1all.A&structure_id2=3dbj.C');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/align?structure_id1=1all.A&bsite1=CYC.175.A.7&structure_id2=3dbj.C&bsite2=CYC.201.C.7');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/align?structure_id1=1all.A&structure_id2=3dbj.C&return=pdb');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/scan?structure_id=5cyt.R');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/scan?structure_id=5cyt.R&bsite=HEM.105.R.5');
#my $request = HTTP::Request->new( GET => 'http://probis.cmm.ki.si/rest/scan?structure_id=5cyt.R&z_score=2.0&return=json');

# 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 returned:\n", $response->content;
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Contact
  • Scientific : konc [at] cmm [dot] ki [dot] si
Release Notes
  • Mar 14 2016: Added color legend for superimposed proteins
  • Feb 23 2016: It is now possible to download the predicted ligands as text file
  • Feb 1 2016: Fixed clustering of protein and nucleic ligands, consequently there are much more in the output