Qnifft 1.2ĭescription: SHEVEK predicts long-range tertiary interactions within RNAs, between RNA-protein and protein-protein interactions from sequence alignments. This program is available from his website. Kim Sharp has developed an updated version of Qnifft that can be compiled for both Linux and SGI platforms. Qnifftĭescription: Qnifft utilizes the non-linear Poisson-Boltzmann (NLPB) equation to calculate the electrostatic potentials of nucleic acids. AMIGOS IIĭescription: AMIGOS II allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures.ĭownloading instructions: AMIGOS II is available at Github or through SBGrid. Note: RCrane and Coot are also available through SBGrid. The source code for RCrane is available on GitHub. Coot downloads are available for Linux, Windows, and Mac. RCrane will then be accessible through the newly-created RCrane menu. Once Coot is launched, go to Extensions -> RCrane launch.
Acta Cryst D68: 958-995 (2012).ĭownloading instructions: RCrane is included in Coot. RCrane: Semi-automated RNA model building. Semiautomated model building for RNA crystallography using a directed rotameric approach. J Mol Biol,(2012).ĭescription: RCrane allows for semi-automated building of RNA structure within Coot.Ĭurrent version: 1.1 (released September 26, 2012) View changelog Discrete RNA Libraries from Pseudo-Torsional Space. Srinivas Somarowthu, Michal Legiewicz, Isabel Chillón Gazquez, Marco Marcia, Fei Liu and Anna Marie Pyleĭiscrete RNA Libraries from Pseudo-Torsional Space.ĭescription: Libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone. Reference: HOTAIR forms an intricate and modular secondary structure Mol Cell 2016 (62) : 111-120 HOTAIR Secondary Structure Nathan Pirakitikulr, Andrew Kohlway, Brett D. Reference: The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures
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