Computing folding pathways between RNA secondary structures

Keywords

Consciousness, Linguistics, Psychology, Ecocriticism, Aesthetics

References

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• Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.A E Walter, Douglas H. Turner, Jinwoong Kim — 1994
• Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.Tianbing Xia, John SantaLucia, Mark E. Burkard — 1998
• Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3'-end triggers structural rearrangements that allow translation and antisense RNA binding.Thomas Franch, Alexander P. Gultyaev, Kenn Gerdes — 1997
• Metrics on RNA Secondary StructuresVincent Moulton, Michael Zuker, Michael Steel — 2000
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• RNA folding pathway functional intermediates: their prediction and analysis.Bruce A. Shapiro, David Bengali, Wojciech K. Kasprzak — 2001
• Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.David H. Mathews, David A. Case — 2006
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• RNA folding at elementary step resolution.Christoph Flamm, Walter Fontana, Ivo L. Hofacker — 1999
• Vienna RNA secondary structure serverIvo L. Hofacker — 2003
• Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.Maumita Mandal, Benjamin J. Boese, Jeffrey E. Barrick — 2003
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Cited by

• Shape-based Barrier Estimation for RNAsSergiy Bogomolov, Martin Mann, Björn Voß — 2010
• A new entropy model for RNA: part IV, The Minimum Free Energy (mFE) and the thermodynamically most-probable folding pathway (TMPFP)Wayne Dawson, Gota Kawai — 2015
• Multi-objective optimization for RNA design with multiple target secondary structuresAkito Taneda — 2015
• A new entropy model for RNA: part III. Is the folding free energy landscape of RNA funnel shaped?Wayne Dawson, Toshikuni Takai, Nobuharu Ito — 2014
• Computing the Partition Function for Kinetically Trapped RNA Secondary StructuresWilliam Andrew Lorenz, Peter Clote — 2011
• RNA folding pathways and kinetics using 2D energy landscapesEvan Senter, Iván Dotú, Peter Clote — 2014
• A new model for approximating RNA folding trajectories and population kineticsBonnie Kirkpatrick, Monir Hajiaghayi, Anne Condon — 2013
• Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational SwitchesEvan Senter, Saad Sheikh, Iván Dotú — 2012
• Predicting folding pathways between RNA conformational structures guided by RNA stacksYuan Li, Shaojie Zhang — 2011
• Analysing RNA-kinetics based on folding space abstractionJiabin Huang, Björn Voß — 2014
• Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular DesignJuan Antonio García-Martín, Peter Clote, Iván Dotú — 2013
• Basin Hopping Graph: a computational framework to characterize RNA folding landscapesMarcel Kucharík, Ivo L. Hofacker, Peter F. Stadler — 2014
• Abstract folding space analysis based on helices.Jiabin Huang, Rolf Backofen, Björn Voß — 2012
• Neural network analysis of mRNA secondary structure across transcriptomesLockhart, E. Gangnon Ronald — 2010
• Efficient procedures for the numerical simulation of mid-size RNA kineticsIddo Aviram, Ilia Veltman, Alexander Churkin — 2012
• Approximating the set of local minima in partial RNA folding landscapesSudhakar Sahoo, Andreas Albrecht — 2012
• Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elementsYuan Li, Cuncong Zhong, Shaojie Zhang — 2014
• Finding stable local optimal RNA secondary structuresYuan Li, Shaojie Zhang — 2011
• Network Properties of the Ensemble of RNA StructuresPeter Clote, Amir H. Bayegan — 2015
• Modelling ribosome kinetics and translational control on dynamic mRNATanel Tammet, Hele-Mai Haav, Vello Kadarpik — 2023

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