Computational Methods for Modeling Aptamers and Designing Riboswitches

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

(2017) Zasha Weinberg et al.   NUCLEIC ACIDS RESEARCH

Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation

(2017) Adrien Chauvier et al.   Nature Communications

The thermodynamics and kinetics of a nucleotide base pair

(2016) Yujie Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Reversible-Switch Mechanism of the SAM-III Riboswitch

(2016) Sha Gong et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Opportunities in the design and application of RNA for gene expression control

(2016) Maureen McKeague et al.   NUCLEIC ACIDS RESEARCH

TheyjdFriboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

(2016) Sanshu Li et al.   RNA

The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts

(2016) Arlie J. Rinaldi et al.   Nature Communications

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction

(2015) Tamaki Endoh et al.   ANALYTICAL CHEMISTRY

iFoldRNA v2: folding RNA with constraints: Fig. 1.

(2015) Andrey Krokhotin et al.   BIOINFORMATICS

Kinetic regulation mechanism of pbuE riboswitch

(2015) Sha Gong et al.   JOURNAL OF CHEMICAL PHYSICS

The regulation mechanism of yitJ and metF riboswitches

(2015) Sha Gong et al.   JOURNAL OF CHEMICAL PHYSICS

Mn 2+ -Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

(2015) Ian R. Price et al.   MOLECULAR CELL

The Ubiquitous yybP-ykoY Riboswitch Is a Manganese-Responsive Regulatory Element

(2015) Michael Dambach et al.   MOLECULAR CELL

High-throughput cellular RNA device engineering

(2015) Brent Townshend et al.   NATURE METHODS

Identifying novel sequence variants of RNA 3D motifs

(2015) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

(2015) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Cotranslational protein folding on the ribosome monitored in real time

(2015) W. Holtkamp et al.   SCIENCE

Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices

(2015) Kathy Y. Wei et al.   Journal of Biological Engineering

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Kinetic partitioning mechanism of HDV ribozyme folding

(2014) Jiawen Chen et al.   JOURNAL OF CHEMICAL PHYSICS

A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

(2014) Ya-Zhou Shi et al.   JOURNAL OF CHEMICAL PHYSICS

Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

(2014) Xiaojun Xu et al.   PLoS One

Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator

(2014) K. Hollands et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Graph-based sampling for approximating global helical topologies of RNA

(2014) N. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Artificial riboswitches for gene expression and replication control of DNA and RNA viruses

(2014) Patrick Ketzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Riboswitch regulates RNA

(2014) J. Chen et al.   SCIENCE

A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator

(2014) S. DebRoy et al.   SCIENCE

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Kinetics of Allosteric Transitions in S-adenosylmethionine Riboswitch Are Accurately Predicted from the Folding Landscape

(2013) Jong-Chin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Differences between cotranscriptional and free riboswitch folding

(2013) Benjamin Lutz et al.   NUCLEIC ACIDS RESEARCH

C o F old : an RNA secondary structure prediction method that takes co-transcriptional folding into account

(2013) Jeff R. Proctor et al.   NUCLEIC ACIDS RESEARCH

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

(2013) Tomasz Puton et al.   NUCLEIC ACIDS RESEARCH

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

(2013) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Sequence-dependent folding landscapes of adenine riboswitch aptamers

(2013) Jong-Chin Lin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

LigandRNA: computational predictor of RNA-ligand interactions

(2013) A. Philips et al.   RNA

Role of Ligand Binding in Structural Organization ofAddA-riboswitch Aptamer: A Molecular Dynamics Simulation

(2012) Zhou Gong et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Kinetic analysis of the effects of target structure on siRNA efficiency

(2012) Jiawen Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch

(2012) Scott P. Hennelly et al.   NUCLEIC ACIDS RESEARCH

De novo design of a synthetic riboswitch that regulates transcription termination

(2012) M. Wachsmuth et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

(2012) G. A. Perdrizet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch

(2012) K. L. Frieda et al.   SCIENCE

Automated and fast building of three-dimensional RNA structures

(2012) Yunjie Zhao et al.   Scientific Reports

Riboswitches: Discovery of Drugs That Target Bacterial Gene-Regulatory RNAs

(2011) Katherine E. Deigan et al.   ACCOUNTS OF CHEMICAL RESEARCH

MetalionRNA: computational predictor of metal-binding sites in RNA structures

(2011) Anna Philips et al.   BIOINFORMATICS

Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars

(2011) Zsuzsanna Sükösd et al.   BMC BIOINFORMATICS

Cotranscriptional folding kinetics of ribonucleic acid secondary structures

(2011) Peinan Zhao et al.   JOURNAL OF CHEMICAL PHYSICS

Variable Sequences outside the Sam-Binding Core Critically Influence the Conformational Dynamics of the SAM-III/SMK Box Riboswitch

(2011) Changrui Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

Automated RNA Structure Prediction Uncovers a Kink-Turn Linker in Double Glycine Riboswitches

(2011) Wipapat Kladwang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

Sequence-based identification of 3D structural modules in RNA with RMDetect

(2011) José Almeida Cruz et al.   NATURE METHODS

Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy

(2011) Bin Chen et al.   NUCLEIC ACIDS RESEARCH

RNA folding in living cells

(2011) Georgeta Zemora et al.   RNA Biology

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression

(2011) J. M. Carothers et al.   SCIENCE

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

(2011) J. L. Baker et al.   SCIENCE

Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms

(2011) Jean-François Lemay et al.   PLoS Genetics

Riboswitch structure in the ligand-free state

(2011) Joseph A. Liberman et al.   Wiley Interdisciplinary Reviews-RNA

R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

(2010) Ryan R. Rahrig et al.   BIOINFORMATICS

Predicting Secondary Structural Folding Kinetics for Nucleic Acids

(2010) Peinan Zhao et al.   BIOPHYSICAL JOURNAL

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

(2010) Mariusz Popenda et al.   BMC BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Tuning Riboswitch Regulation through Conformational Selection

(2010) Ross C. Wilson et al.   JOURNAL OF MOLECULAR BIOLOGY

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

BarMap: RNA folding on dynamic energy landscapes

(2010) I. L. Hofacker et al.   RNA

Riboswitches and the RNA World

(2010) R. R. Breaker   Cold Spring Harbor Perspectives in Biology

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

(2009) Magdalena A. Jonikas et al.   BIOINFORMATICS

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm

(2009) Wei Huang et al.   NUCLEIC ACIDS RESEARCH

MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch

(2009) M. Sharma et al.   RNA

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Folding Kinetics of Large RNAs

(2008) Michael Geis et al.   JOURNAL OF MOLECULAR BIOLOGY

Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers

(2008) Jong-Chin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Structure of the SAM-II riboswitch bound to S-adenosylmethionine

(2008) Sunny D Gilbert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes

(2008) C. Hyeon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA