Database of protein-nucleic acid binding pairs at atomic and residue levels

Abstract

As the number of structures of protein-DNA complexes and protein-RNA complexes that have been solved has been increased substantially for the past few years, a large amount of structure data is available at several resources. However, the information on the binding sites between protein and nucleic acid is not readily available from the structure data, which consist mostly of the three-dimensional coordinates of the atoms in the complexes. A few databases constructed recently provide the information on protein-nucleic acid interface, but most of them provide binding sites on either side (protein or nucleic acid) rather than binding pairs on both sides. This paper presents a new database of protein-nucleic acid binding pairs at various levels. The binding pairs identified from an extensive analysis of protein-DNA complexes and protein-RNA complexes will provide a valuable resource for studying protein-nucleic acid interactions. The database is available at http://bclab.inha.ac.kr/dbbp. © Springer-Verlag Berlin Heidelberg 2013.