BIPA, a database for protein-nucleic acid interaction, provides various features of protein-nuleic acid interfaces. As of Wednesday 10 Feb 2010, there are 2333 protein-nucleic acid PDB complexes (Lac repressor, Cro, p53, and etc.), 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids. All by all shape similarities among protein-nucleic acid interfaces were calculated using USR method, which enables us to navigate similar interfaces across the families.

Furthermore, by relating BIPA to our in-house databases such as Double-map, UniProt annotations were mapped onto the nucleic acid-binding proteins to provide additional information and potential candidates of mutations which might be affecting protein-nucleic acid interactions.