NPDock: A web server for protein-nucleic acid docking

Abstract

Protein-RNA and protein-DNA interactions play fundamental roles in many biological processes. A detailed understanding of these interactions requires knowledge about protein-nucleic acid complex structures. Because the experimental determination of these complexes is time-consuming and perhaps futile in some instances, we have focused on computational docking methods starting from the separate structures. Docking methods arewidely employed to study protein-protein interactions; however, only a few methods have been made available to model protein-nucleic acid complexes. Here, we describe NPDock (Nucleic acid-Protein Docking); a novel web server for predicting complexes of protein-nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. The smallest set of input data consists of a protein structure and a DNA or RNA structure in PDB format. Advanced options are available to control specific details of the docking process and obtain intermediate results. The web server is available at http://genesilico.pl/NPDock.