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 are widely 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.

Figure 1.

The workflow of the NPDock server.

Figure 2.

The NPDock result of docking of an apo-form of the Norwalk virus polymerase structure (PDB code: 1SH0) and dsRNA taken from that complex (PDB code: 3BSO): (1) a list of the refined best scored complexes, (2) raw files for each step of the docking can be viewed by clicking the links, (3) JSmol 3D visualization of the best scored complex, (4) a plot illustrating how the score changes during a simulation, (5) detailed information about each step of the docking can be viewed by clicking the ‘Show the full log’ button and (6) a detailed explanation of the result that can be viewed by clicking the ‘Explain results’ button.