# NPDock: a web server for protein–nucleic acid docking

## TL;DR

NPDock is a web server that predicts how proteins interact with DNA or RNA using computational methods, helping researchers understand these interactions without needing experimental data.

## Contribution

NPDock introduces a novel, user-friendly web server for modeling protein–nucleic acid complexes with a complete computational workflow.

## Key findings

- NPDock implements a workflow including docking, scoring, clustering, and refinement of protein–nucleic acid complexes.
- The server provides 3D visualization and advanced options for controlling the docking process.
- It requires only PDB-formatted protein and nucleic acid structures as minimal input.

## 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.