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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;
ProBiS in Brief
Query structure is shown in Jmol colored by the degrees of structural conservation.
Structurally conserved residues (red) correspond with the GDP binding site.
Local pairwise structural alignment of two differently folded proteins.
Similar proteins are ranked by Z-Scores. A red star indicates different Protein Family (Pfam) than that of query.
Local pairwise structural alignment is presented as a table of residue-residue correspondences.
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ProBiS is developed at the National Institute of Chemistry, Ljubljana, Slovenia