RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Natalia Szostak,Janusz M Bujnicki,Kristian M Rother,Michal J Pietal

doi:10.1186/1471-2105-13-333

Natalia Szostak, Janusz M Bujnicki + Show 2 more

Open Access

https://doi.org/10.1186/1471-2105-13-333

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Abstract

BackgroundThe structures of biological macromolecules provide a framework for studying their biological functions. Three-dimensional structures of proteins, nucleic acids, or their complexes, are difficult to visualize in detail on flat surfaces, and algorithms for their spatial superposition and comparison are computationally costly. Molecular structures, however, can be represented as 2D maps of interactions between the individual residues, which are easier to visualize and compare, and which can be reconverted to 3D structures with reasonable precision. There are many visualization tools for maps of protein structures, but few for nucleic acids.ResultsWe developed RNAmap2D, a platform-independent software tool for calculation, visualization and analysis of contact and distance maps for nucleic acid molecules and their complexes with proteins or ligands. The program addresses the problem of paucity of bioinformatics tools dedicated to analyzing RNA 2D maps, given the growing number of experimentally solved RNA structures in the Protein Data Bank (PDB) repository, as well as the growing number of tools for RNA 2D and 3D structure prediction. RNAmap2D allows for calculation and analysis of contacts and distances between various classes of atoms in nucleic acid, protein, and small ligand molecules. It also discriminates between different types of base pairing and stacking.ConclusionsRNAmap2D is an easy to use method to visualize, analyze and compare structures of nucleic acid molecules and their complexes with other molecules, such as proteins or ligands and metal ions. Its special features make it a very useful tool for analysis of tertiary structures of RNAs. RNAmap2D for Windows/Linux/MacOSX is freely available for academic users at http://iimcb.genesilico.pl/rnamap2d.html

Highlights

The structures of biological macromolecules provide a framework for studying their biological functions
Based on our previous experience with protein 2D map analysis and core parts of the PROTmap2D code [13], we developed RNAmap2D, a standalone tool for calculation, visualization and analysis of contact and distance maps of nucleic acid structures and structures of protein-nucleic acid complexes
RNAmap2D is a new tool for calculation and visualization of nucleic acid contact and distance maps

Summary

Introduction

The structures of biological macromolecules provide a framework for studying their biological functions. RNAs and proteins are linear polymers composed of a limited set of building blocks (ribonucleotide and amino acid residues, respectively) that may spontaneously fold into complex three-dimensional shapes [1,2]. In both RNA and proteins, the order of building blocks held together by covalent bonds is called the primary structure, the local conformation of the chain stabilized mostly by. While three-dimensional macromolecular structures represent an information-rich framework for studying biological functions, visualizing and analyzing them is difficult both for humans and computer programs. Contact maps can be enriched with additional information, e.g. to discriminate different types of contacts or to indicate the chirality in 3D (handedness), which is otherwise lost upon the conversion to a 2D representation

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