Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces
In the current version, Nabe contains 2,506 mutations in 336 protein-DNA AND 137 protein-RNA complexes, supplemented with experimental conditions, literature, structural and functional information, and links to other databases for protein sequence, structure, and interaction network.
Figure 1 shows the schematic diagram describing data collection, workflow and applications of Nabe database. We use the following steps to collect the mutagenesis data: (i) Initially, we cluster all the PDB entries of protein-nucleic acid complexes from the PDB database. (ii) For each PDB entry, we extract from the PDB database the corresponding literature that is the first one to depict the information about the complex in detail. (iii) Then we use the corresponding literatures as the beginning points to search for ample references concerning mutation experiments, because the subsequent measurements of binding free energy generally would cite the initial articles with sequence and structural information of the corresponding complexes. Specifically, we use Google Scholars to locate all the literatures that cite the original ones, and filter the results with some keywords (such as mutations, mutation Kd and mutation ΔG) to limit the scope of the query. (iv) Finally, we review each paper to manually extract experimental mutagenesis data and calculate the binding free energy change. Our focus is mainly on the method section, result section, tables and charts of every article and supplementary material. In addition, as we observe that most protein-nucleic acid hot spots prediction methods construct their data sets by merging different databases or downloading data from former models, we incorporate similar databases and data sets, such as dbAMEPNI and ProNIT etc., into Nabe database to further expand the data volume and, more significantly, help researchers save time in gathering data.
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