[Github repositories for Pyle lab software]
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
RCrane
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.
AMIGOS II
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: AMIGOS II is available at Github or through SBGrid.
Qnifft
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
SHEVEK
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: SHEVEK is available on Github.
Old Versions of Software