Nucleic Acids Research, 2012, Vol. 40, Web Server issue W523 Figure 2. Antigen-binding regions identiﬁcation. (A) The sequence of the query Ab is BLASTed against the non-redundant set of annotated Abs. (B) The framework regions (FRs) of the best BLAST hit Ab are aligned to the query Ab (sequences—BLAST, structures—CE). (C) The ABRs of the query Ab are inferred according to the ABRs of the best BLAST hit Ab. Table 1. Comparative performance of Paratome and the most commonly used CDR identiﬁcation methods Measure/Method Recall Precision Speciﬁcity Paratome (%) 94 42 83 Kabat (%) 85 41 85 Chothia (%) 79 44 89 IMGT (%) 81 48 91 Average precision, recall and speciﬁcity were calculated for the Abs in the test set for Paratome, Kabat, Chothia and IMGT methods. construction of the training set. For the full list of train and test sets is available at http://ofranservices.biu.ac.il/ site/services/paratome/ABRs_train_pdb.txt, 23 May 2012, date last accessed http://ofranservices.biu.ac.il/site/ services/paratome/ABRs_test_pdb.txt, 23 May 2012, date last accessed). A true positive (TP) prediction is a residue that is included in the ABRs and is in contact with the Ag in the experimentally determined structure of the Ab–Ag complex. A true negative (TN) is a residue that is not in the ABR and is not in contact with the Ag. A false positive (FP) is a residue that is in the ABR and not in contact with the Ag in the experimental structure and a false negative (FN) is a residue that is not in the ABR and is in contact with the Ag. The performance was assessed in terms of pre- cision (TP/TP+FP), speciﬁcity (TN/TN+FP) and recall (TP/TP+FN). Additionally, performance was compared to that of CDRs, as identiﬁed by Kabat, Chothia and IMGT. CDRs according to Kabat and Chothia were obtained by coupling the Abnum tool (http://www .bioinf.org.uk/abs/abnum/, 23 May 2012, date last accessed) with a table of CDRs deﬁnitions (http://www. bioinf.org.uk/abs/#cdrdef, 23 May 2012, date last accessed). To obtain the CDRs according to IMGT, we applied the IMGT-gap tool (http://www.imgt.org/ 3Dstructure-DB/cgi/DomainGapAlign.cgi, 23 May 2012, date last accessed). An Ab amino acid and an Ag amino acid were considered as interacting if at least one of their respective atoms were 6 A˚ of each other (23). Table 1 summarizes the performance obtained by all methods on the test set. While the precision of all methods is roughly the same, the results show that virtually all Ag-binding residues fall within the ABRs predicted by Paratome. IMPLEMENTATION The server was designed and implemented using Perl, bash, Python, HTML, XML and XSL. The front end of the server is designed in HTML, XML and XSL. Structure visualization is enabled using the Jmol Java applet (http:// jmol.sourceforge.net/, 23 May 2012, date last accessed). The web server and computations run on a Red-hat Enterprise Linux 5.7 (Tikanga) with 3.00 GHz 8 CPUs and 16 GB primary memory. CONCLUSION The speciﬁcity and afﬁnity of Ab–Ag interactions are fun- damental for understanding the biological activity of these molecules. Correct identiﬁcation of the residues that mediate these interactions is crucial for immunological