Sunday, March 3, 2013

DSSR: Software for Defining the (Secondary) Structures of RNA

As the number of experimentally solved RNA-containing structures grows, it is becoming increasingly important to characterize the geometric features of the molecules in a consistent and efficient manner. Here comes DSSR, a software for Defining the (Secondary) Structures of RNA. See the post titled "DSSR, what's it and why bother?" for more info.

Starting from an RNA structure in PDB format, DSSR employs a set of simple rules to identify all existent base pairs (bp): both canonical Watson–Crick pairs and non-canonical pairs with one or more H-bonds, made up of normal or modified bases, regardless of tautomeric or protonation state. The classification is based on the six standard rigid-body bp parameters (shear, stretch, stagger, propeller, buckle, and opening), which together rigorously quantify the spatial disposition of the two interacting bases. The program characterizes each bp not only by common pattern names (Watson-Crick, wobble, Hoogsteen, sheared, dinucleotide platform), but also according to the Saenger classification scheme of 28 types and the Leontis-Westhof nomenclature of 12 basic geometric classes.

DSSR detects triplets, quadruplets, and even higher-order base associations by searching horizontally in the planes of the associated bases for further H-bonding interactions. The program determines helical regions by exploring each bp’s neighborhood vertically for base-stacking interactions regardless of backbone connection (e.g., coaxial stacking of helices). DSSR calculates commonly used backbone (including the virtual eta/theta) torsion angles, identifies A-minor interactions (type I and II), G quartets, and bulges, internal loops and multi-branch loops. It also detects the existence of pseudo-knots, and outputs RNA secondary structure in dot-bracket notation.

The program is implemented in ANSI C as a stand-alone command-line program with zero dependencies on third-party libraries. No setup is necessary; simply put it into a directory of your choice (preferably one in your command PATH), and it will run. DSSR is a new component of the 3DNA suite of programs ( for the analysis, rebuilding, and visualization of three‐dimensional nucleic acid structures.

DSSR is currently released in beta testing version; nevertheless, it should already be robust and efficient enough for real-world applications. I am actively improving the software, and would greatly appreciate your feedback. Give it a try, and report back on the 3DNA Forum any issues you have!