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[ccp4bb] DSSR: Software for Defining the (Secondary) Structures of RNA



We are pleased to announce the beta testing release of DSSR
(http://forum.x3dna.org/rna-structures/): a software program for
Defining the (Secondary) Structures of RNA. DSSR is implemented in ANSI
C as a stand-alone command-line program, and is self-contained. Compiled
versions for Linux (32bit/64bit), Mac OS X, and Windows (MinGW/Cygwin)
are available from the 3DNA Forum site (http://forum.x3dna.org/), and
the executables have zero dependencies on third-party libraries to run.
The download size is tiny (~0.5MB) and no setup is necessary: simply put
the program into a folder of your choice (preferably one on your command
PATH), and it *should* work.

Starting from an RNA structure in PDB format, DSSR employs a set of
simple criteria to identify all existent base pairs (bp): both canonical
Watson–Crick (WC) 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 any two interacting bases. Moreover, the program characterizes each
bp by commonly used names (WC, reverse WC, Hoogsteen, reverse Hoogsteen,
wobble, sheared, imino, Calcutta, dinucleotide platform), the Saenger
classification scheme of 28 types, and the Leontis-Westhof nomenclature
of 12 basic geometric classes.

DSSR detects triplets, quadruplets, and higher-order base associations
by searching horizontally in the plane of the associated bp 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, or pseudo helices). DSSR calculates commonly used backbone
(including the virtual eta/theta) torsion angles, identifies A-minor
interactions (types 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 structures in the dot-bracket notation.

The program is currently under active development. Nevertheless, the
beta testing version has been checked against all RNA/DNA-containing
entries in the PDB as of March 2013, and should be robust enough for
real-world applications. As always, we greatly appreciate your feedback.
Please report all DSSR-related issues to the open 3DNA Forum website
(http://forum.x3dna.org/), and I strive to promptly respond to any
questions posted there.

[Posted to CCP4BB and pdb-l mailing list on Monday, 2013-03-11]

Xiang-Jun

PS. DSSR is a new component of the 3DNA (http://x3dna.org/) suite of
    programs for the analysis, rebuilding, and visualization of
    three‐dimensional nucleic acid structures.

--
Xiang-Jun Lu (PhD)
Email: xiangjun@x3dna.org
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/