Abstract Summary:BIPA is a database for protein–nucleic acid interactions in 3D structures. The database provides various physicochemical features of protein–nucleic acid interface such as size, shape, residue propensity, secondary structure composition and intermolecular interactions. The database also contains multiple structural alignments of nucleic acid-binding protein families with annotations of local environments in order to allow definition of features that influence acceptability of mutations at a particular position in a protein family. A web interface has been designed to present the results of these analyses and facilitate navigation of protein–nucleic acid interfaces. Availability: http://www-cryst.bioc.cam.ac.uk/bipa Contact: semin@cryst.bioc.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.