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.