R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes.

Abstract

There are over 21,000 atomic-resolution 3D structures containing RNA and/or DNA chains in the Protein Data Bank, ranging in size from 2 nt to tens of thousands. Most structures have more than one nucleic acid chain, and many have multiple models, assemblies, or symmetry operators. Nucleic acid 3D structures are formed by repetition of Watson-Crick base pairs and base stacking, but RNA (and increasingly DNA) is also shaped by non-Watson-Crick base pairs and various base-backbone interactions. It is difficult to comprehend the entirety of the interactions that form within and between chains in complex 3D structures; for example, there are several chains, over 5500 nt, and over 9700 pairwise interactions in one human ribosomal RNA 3D structure. Here we introduce R3DCID (RNA + DNA 3D structure Circular Interaction Diagram, pronounced "red sid"), a web service that produces circular arc representations of the pairwise interactions in all chains, models, assemblies, and symmetries in each nucleic acid structure in PDB. Diagrams have a uniform appearance and interpretation across all sizes and varieties of structures. Output is provided in PDF and SVG format for compact file sizes and smooth zooming and panning. R3DCID provides a new perspective on nucleic acid 3D structures; it serves as a guide to their overall structure and as a detailed map of the interactions that are critical to their function.