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.
Highlights
Proteins and nucleic acids are the two main types of biological macromolecules that often tend to function together in the cell
NPDock is implemented as a computational workflow that consists of the GRAMM program, which is a thirdparty method [19], and a set of tools developed mainly in our laboratory, including the DARS-RNP and QUASIRNP statistical potentials for scoring protein–RNA complexes with coarse-grained representation [15], a counterpart of QUASI-RNP for scoring protein–DNA complexes (QUASI-DNP), and tools for clustering, selection and refinement of models (Figure 1)
The server was launched in December 2013 as RNPdock and had the capability to dock protein–RNA complexes with the use of the DARS-RNP and QUASI-RNP potentials [15]
Summary
Proteins and nucleic acids are the two main types of biological macromolecules that often tend to function together in the cell. Protein–RNA and protein–DNA interactions play a fundamental role in a variety of biological processes, including DNA replication, RNA transcription, RNA splicing, degradation of nucleic acids and protein synthesis. These interactions are essential to cellular metabolism and the survival of all organisms. Defects in protein–nucleic acid interactions are implicated in a number of diseases, ranging from neurological disorders to cancer [1,2] Our understanding of these processes will improve as new structures of protein–nucleic acid complexes are solved and the structural details of the interactions are analyzed. Experimental determination of most protein–nucleic acid complex structures by high-resolution methods is a tedious and difficult process [3]
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