I'm pleased to announce the release of DSSR v1.0.3, a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates (http://goo.gl/ap12xJ). Since its initial beta release in early March 2013, I've continuously refined the program by taking user feedback into consideration. DSSR is now mature and stable, with a 45-page long user manual and a simple web interface (http://web.x3dna.org/).
Given an RNA structure in PDB or PDBx/mmCIF format, DSSR identifies the Watson–Crick, wobble, and non-canonical base pairs in the structure. It classifies the pairs by standard parameters, common names, and popular nomenclature (e.g., Saenger and Leontis-Westhof). DSSR detects multiplets (triplets or higher-order base associations), and double helical regions regardless of backbone connection. The program identifies hairpin loops, bulges, internal loops, and multi-branch loops (junctions), and recognizes the existence of pseudo-knots. DSSR outputs RNA secondary structure in dot-bracket notation (.dbn) and connect table format (.ct). DSSR calculates commonly used backbone torsion angles, classifies the backbone conformations, and assigns the consensus RNA backbone suite names. The program also identifies A-minor interactions, ribose zippers, G quartets, kissing loops, U-turns, and kink-turns. Furthermore, the output includes non-pairing interactions and contacts involving phosphate groups. Implemented in C as a standalone command-line program, DSSR is self-contained and the executable is tiny (~0.7mb), with zero runtime dependencies on third-party libraries. DSSR is a new component of the 3DNA suite of programs (http://x3dna.org/) for the analysis, rebuilding, and visualization of three‐dimensional nucleic acid structures. It consolidates, refines, and significantly extends 3DNA's functionality for RNA structural analysis. DSSR is currently distributed in binary forms for Linux, Mac OS X, and Windows, which can downloaded from the 3DNA Forum (http://forum.x3dna.org/). The program is being actively maintained. Any DSSR-related problems are welcome on the form, and will be promptly addressed. [Posted to CCP4BB and the pdb-l mailing list on Monday, 2014-03-10] Xiang-Jun -- Xiang-Jun Lu (PhD) Email: [email protected] Web: http://x3dna.org/ Forum: http://forum.x3dna.org/
