Thermodynamic database for protein-nucleic acid interactions (ProNIT)

Motivation: Protein-nucleic acid interactions are fundamental to the regula tion of gene expression. In order to elucidate the molecular mechanism of p rotein-nucleic acid recognition and analyze the gene regulation network, no t only structural data but also quantitative binding data are necessary. Al though there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data. Thus, we have deve loped a Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNI T). Results: We have collected experimentally observed binding data from the li terature. ProNIT contains several important thermodynamic data for protein- nucleic acid binding, such as dissociation constant (K-d), association cons tant (K-a), Gibbs free energy change (DeltaG), enthalpy change (DeltaH), he at capacity change (DeltaC(p)), experimental conditions, structural informa tion of proteins, nucleic acids and the complex, and literature information . These data are integrated into a relational database system together with structural and functional information to provide flexible searching facili ties by using combinations of various terms and parameters. A www interface allows users to search for data based on various conditions, with differen t display and sorting options, and to visualize molecular structures and th eir interactions.