HCV Secondary Structure

Data: HCV structure

Reference: The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures
Nathan Pirakitikulr, Andrew Kohlway, Brett D. Lindenbach and Anna Marie Pyle
Mol Cell 2016 (62) : 111-120

HOTAIR Secondary Structure

Data: HOTAIR structure

Reference: HOTAIR forms an intricate and modular secondary structure
Srinivas Somarowthu, Michal Legiewicz, Isabel Chillón Gazquez, Marco Marcia, Fei Liu and Anna Marie Pyle
Mol Cell 2015 (58) : 353-361

Discrete RNA Libraries from Pseudo-Torsional Space.

Author: Elisabeth Humphris 
Description: Libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone.
Reference: Humphris E and Pyle AM. Discrete RNA Libraries from Pseudo-Torsional Space. J Mol Biol,(2012).
Download: RNA Libraries

—new below


Author: Kevin Keating

Description: RCrane allows for semi-automated building of RNA structure within Coot.
Current version: 1.1 (released September 26, 2012) View changelog
References: Keating KS and Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA, 107 (2010) 8177-8182.
Keating KS and Pyle AM. RCrane: Semi-automated RNA model building. Acta Cryst D68: 958-995 (2012).

Downloading instructions: RCrane is included in Coot. Once Coot is launched, go to Extensions -> RCrane launch. RCrane will then be accessible through the newly-created RCrane menu. Coot downloads are available for Linux, Windows, and Mac. The source code for RCrane is available on GitHub.

Note: RCrane and Coot are also available through SBGrid.


Author: Leven Wadley

Description: AMIGOS II allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.

Downloading instructions: Please contact us if you would like to use AMIGOS II . You will be required to sign a license agreement, and then we will provide the software and installation instructions by email. It is free for academic use but carries a charge for industrial use.

Note: AMIGOS II is also available through SBGrid.


Description: Qnifft utilizes the non-linear Poisson-Boltzmann (NLPB) equation to calculate the electrostatic potentials of nucleic acids.

Qnifft 1.4/2.2

Kim Sharp has developed an updated version of Qnifft that can be compiled for both Linux and SGI platforms. This program is available from his website.

Qnifft 1.2

Download: qnifft.tar.gz


Author: Phillip S. Pang

Description: SHEVEK predicts long-range tertiary interactions within RNAs, between RNA-protein and protein-protein interactions from sequence alignments.

Reference: “Prediction of Functional Tertiary Interactions and Intermolecular Interfaces From Primary Sequence Data”, PS Pang, E Jankowsky, LM Wadley and AM Pyle, J of Experimental Zoology (Mol Dev Evol) (2005), 000, 1-14.

Downloading instructions: Please contact us if you would like to use SHEVEK.

Old Versions of Software