Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces

Protein-nucleic acid complexes play essential roles in regulating transcription, translation, DNA replication, repair and recombination, RNA processing and translocation. Site-directed mutagenesis has been extremely useful in understanding the principles of protein-DNA and protein-RNA interactions, and experimentally determined mutagenesis data are prerequisites for designing effective algorithms for predicting the binding affinity change upon mutation. However, a vital challenge in this area is the lack of sufficient public experimentally recognized mutation data, which leads to difficulties in developing computational prediction methods. In this article, we present Nabe, an integrated database of amino acid mutations and their effects on the binding free energy in protein-DNA and protein-RNA interactions for which binding affinities have been experimentally determined. Compared with existing databases and data sets, Nabe is the largest protein-nucleic acid mutation database, containing 2506 mutations in 473 protein-DNA and protein-RNA complexes, and of that 1751 are alanine mutations in 405 protein-nucleic acid complexes. For researchers to conveniently utilize the data, Nabe assembles protein-DNA and protein-RNA benchmark databases by adopting the data-processing procedures in the majority of models. To further facilitate users to query data, Nabe provides a searchable and graphical web page. Database URL: http://nabe.denglab.org.