W218 Nucleic Acids Research, 2012, Vol. 40, Web Server issue ProBiS web services The new ProBiS web server uses RESTful web services to provide ready access from user scripts to the binding site similarities and local pairwise alignments for any PDB protein structure (30). Speciﬁcation of the web services interface input data, a full set of commands and useful examples can be found at the ‘ProBiS-Web server RESTful Web Services’ instructions page at http:// probis.cmm.ki.si/?what=webservices. The results of the web services calculations are returned in XML, Json or PDB formats, which are well supported in modern programming languages. NEW FEATURES IN THE 2012 ProBiS WEB SERVER Faster calculation In 2010, a batch script ran the non-parallel version of the ProBiS algorithm on 16 processors of a single computer (25). In 2012, the ProBiS algorithm (26) was parallelized using the Open-MPI library, and now runs on 250 pro- cessors of the ProBiS web server, which has shortened search time from hours to minutes. Integration with the ProBiS-Database The new ProBiS web server features integrated access to the ProBiS-Database (27), which is a searchable repository of local pairwise alignments of non-redundant protein structures (nr-PDB) generated by the ProBiS algorithm. This database consists of 420 million pre-calculated pair-wise alignments and presents a faster alternative to the standard de novo protein similarity detection used by the ProBiS web server: structural similarity results are obtained in seconds from the ProBiS-Database. However, the database holds results only for the 29 000 nr-PDB proteins; for non-nr-PDB proteins, results are for the closest homologue in the nr-PDB. Improved user interface New features in ProBiS include: (i) submission of a binding site as a query—previously only complete proteins could be used as queries; (ii) comparison of the query protein against a user-provided list of PDB/Chain IDs. Previously, this was possible only against proteins in the nr-PDB; (iii) links to other protein annotation resources, such as Pfam, SCOP or UniProt; (iv) extended download options—results can be downloaded as CSV, XML, Json Figure 4. Superimposition of similar binding sites in Ddl (1iov.A; blue) and PKC (1xjd.A; violet). The superimposed residues from Ddl and protein kinase C are shown as thin wireframe models. The co-crystallized ligands, ADP (blue) and staurosporine (violet), are shown as thick wireframe models.