W214–W221 Nucleic Acids Research, 2012, Vol. 40, Web Server issue doi:10.1093/nar/gks435 Published online 16 May 2012 ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins Janez Konc and Dusˇ anka Janezˇ icˇ * National Institute of Chemistry, Ljubljana, Slovenia Received February 18, 2012; Revised April 17, 2012; Accepted April 25, 2012 ABSTRACT The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at de- tection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old- version, and the new ProBiS web server is at http://probis.cmm.ki.si. INTRODUCTION Detection of structural similarities in proteins can be applied to many open questions. These include elucidation of the biochemical functions of newly characterized proteins (1–4), identiﬁcation of novel indications for existing drugs—drug repositioning (5–7), and prediction of interactions of known drugs with secondary targets, or off-targets that may lead to undesirable side effects (8,9). However, comparison of only the sequence and folding of proteins fails to address these problems because protein binding sites, rather than protein folding, control interaction with ligands and hence bio- chemical function (10). Web servers that allow the detec- tion of local similarities in proteins have been developed (11–21), and there is an increasing number of approaches that deal with drug repositioning and off-target prediction from different perspectives (22–24). Two programs developed at the National Institute of Chemistry in Ljubljana, ProBiS web server (25,26) and ProBiS-Database (27) enable the detection of structurally similar protein binding sites and local pairwise alignment of crystallographically or NMR determined protein structures from the PDB. ProBiS-Database holds pre- calculated structural similarity proﬁles for over 29 000 non-redundant proteins in the PDB, and allows access to these results in seconds. The ProBiS web server allows de novo similarity calculations, using the ProBiS algorithm, for any protein in the PDB. ProBiS is different from most other structural alignment algorithms, in that it can align proteins having different folds, if they share similar binding sites. ProBiS conducts searches for similar three-dimensional structural regions in proteins without reference to known binding sites or co-crystallized ligands, and takes into account entire protein surfaces. It accepts a protein struc- ture as a query, and compares it against each protein in the non-redundant PDB (nr-PDB). The nr-PDB, updated weekly, is derived from the entire PDB which currently has 182 000 protein single chain structures (28). All these single chain protein structures are clustered with >95% sequence identical structures and a representative of each cluster is chosen. These 29 000 representatives identiﬁed in this way, constitute the nr-PDB; each is identiﬁed with a PDB number and chain, as in 2q4u.A. The ProBiS algorithm represents the surfaces of compared proteins as protein graphs, i.e. structures of vertices and edges, the vertices corresponding to functional groups of surface amino acid residues and the edges determined by distances between pairs of adjacent vertices. This represen- tation captures both geometric as well as physicochemical characteristics of protein surfaces. ProBiS compares the query protein to each of the database proteins, using the maximum clique algorithm (29), which allows it to efﬁ- ciently detect the largest similar subgraphs of compared *To whom correspondence should be addressed. Tel: +386 1 476 0321; Fax: +386 1 476 0300; Email: dusa@cmm.ki.si The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.