[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



Author: Chengxin Zhang

Description: Universal Structure Alignment of RNAs, DNAs, proteins and macromolecule complexes.
References: Zhang C, Shine M, Pyle AM, Zhang Y. US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes. Nat Methods (2022).

Download instructions: The source code can be downloaded from Github or the US-align web-server.



Author: Chengxin Zhang

Description: CSSR assigns RNA secondary structure to coarse-grained tertiary structure.
References: Zhang C and Pyle AM. CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures . Acta Cryst D (2022).

Download instructions: The source code and binary executable for Linux, Mac and Windows can be downloaded from Github.



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).

Download 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: Morgan Shine & Chengxin Zhang

Description: AMIGOS III allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures within the PyMOL molecular graphic system.

Download instructions: AMIGOS III is available as a PyMOL plugin at Github. An older version of AMIGOS II is available as a standalone Java applet at Github or 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.

Download instructions: SHEVEK is available on Github.

Old Versions of Software