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 https://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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Most Recent Citation

Konc, J., Miller, B. T., Stular, T., Lesnik, S., Woodcock, H. L., Brooks, B. R., and Janezic, D. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model., 2015, 55, 2308-2314.

Related Citations

Konc,J. and Janezic,D. ProBiS–ligands: a web server for prediction of ligands by examination of protein binding sites. Nucleic Acids Res., 2014, 42, W215-W220.
Konc,J. and Janezic,D. ProBiS–2012: web server and web services for detection of structurally similar binding sites in proteins. Nucleic Acids Res., 2012, 40, W214-W221.
Konc,J., Cesnik,T., Trykowska Konc,J., Penca,M., Janezic,D. ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures. J. Chem. Inf. Model., 2012, 52, 604-612.
Konc,J. and Janezic,D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics, 2010, 26, 1160-1168.
Konc,J. and Janezic,D. ProBiS: a web server for detection of structurally similar protein binding sites. Nucleic Acids Res., 2010, 38, W436-W440.
Konc,J. and Janezic,D. Protein-protein binding-sites prediction by protein surface structure conservation. J. Chem. Inf. Model., 2007, 47, 940-944.
Konc,J. and Janezic,D. An improved branch and bound algorithm for the maximum clique problem. MATCH Commun. Math. Comput. Chem., 2007, 58, 569-590.

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.

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).
Get Representative Translate your PDB & Chain ID to > 95% sequence identical representative: /rest/get_representative?structure_id=1ytf.A
Get Local Structural Alignments Get local structural alignments with Z-Scores>2.0 for a representative: /rest/get_alignments?structure_id=1ytb.B&z_score=2.0
Get Superimposition Get the PDB file of two superimposed representative structures: /rest/get_superimposition?structure_id1=1all.A&structure_id2=3nmd.B&alignment_no=1
Get Similarity Scores Get 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
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;

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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

ProBiS-Database Access

The ProBiS-Database Widget

Widget:

Usage:

Options:

The ProBiS-Database RESTful Web Service Interface

Get Representative

Get Local Structural Alignments

Get Superimposition

Get Similarity Scores

Perl Example Script