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
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.
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.
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.