Protein and nucleic acid interactions play a vital role in many biological processes such as DNA replication, repair and processing, as well as RNA processing and translocation. Computational alanine scanning has been developed as a complementary approach for the prediction of energetically dominant amino acid residues (hot spots) in protein complex interfaces. Hotspots In silico Scanning on Nucleic Acid and Protein Interface (HISNAPI) Web Server provides fast and accurate predictions for the effects of single alanine substitutions on the binding free energy of protein-nucleic acid complex. The method has considered the conformational flexibility of protein-nucleic acid complex by sampling conformations using molecular dynamics simulation. And an empirical force field FoldX has been utilized to determine the binding energy of wild-type and mutant protein-nucleic complex. Our method has been tested on a set of experimental mutagenesis data and the results demonstrated that it is capable of anticipating the experimental results.