Consistent global structures of complex RNA states through multidimensional chemical mapping

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

Standardization of RNA Chemical Mapping Experiments

(2014) Wipapat Kladwang et al.   BIOCHEMISTRY

Characterizing the Dynamics of the Leader–Linker Interaction in the Glycine Riboswitch with Site-Directed Spin Labeling

(2014) Jackie M. Esquiaqui et al.   BIOCHEMISTRY

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

(2014) Kyle A. Beauchamp et al.   BIOPHYSICAL JOURNAL

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Structural basis for diversity in the SAM clan of riboswitches

(2014) J. J. Trausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation of a group I intron into a lariat capping ribozyme

(2014) M. Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From a structural average to the conformational ensemble of a DNA bulge

(2014) X. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy

(2014) Karen M. Ruff et al.   RNA

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states

(2014) Siqi Tian et al.   RNA

Advances in the Determination of Nucleic Acid Conformational Ensembles

(2013) Loïc Salmon et al.   Annual Review of Physical Chemistry

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

(2013) Jinwei Zhang et al.   NATURE

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

(2013) Hanjoo Kim et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric Tertiary Interactions Preorganize the c-di-GMP Riboswitch and Accelerate Ligand Binding

(2012) Sharla Wood et al.   ACS Chemical Biology

Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

(2012) Pablo Cordero et al.   BIOCHEMISTRY

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch

(2012) Alla Peselis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Accurate protein structure modeling using sparse NMR data and homologous structure information

(2012) J. M. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

(2012) F. Karabiber et al.   RNA

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

Ultraviolet Shadowing of RNA Can Cause Significant Chemical Damage in Seconds

(2012) Wipapat Kladwang et al.   Scientific Reports

Understanding the Errors of SHAPE-Directed RNA Structure Modeling

(2011) Wipapat Kladwang et al.   BIOCHEMISTRY

HiTRACE: high-throughput robust analysis for capillary electrophoresis

(2011) Sungroh Yoon et al.   BIOINFORMATICS

Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

(2011) Ethan B. Butler et al.   CHEMISTRY & BIOLOGY

Constructing Accurate Contact Maps for Hydroxyl-Radical-Cleavage-Based High-Throughput RNA Structure Inference

(2011) Jinkyu Kim et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

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

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

A two-dimensional mutate-and-map strategy for non-coding RNA structure

(2011) Wipapat Kladwang et al.   Nature Chemistry

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

(2011) P. Sripakdeevong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

Riboswitch function: Flipping the switch or tuning the dimmer?

(2010) Nathan J. Baird et al.   RNA Biology

Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

(2010) T. V. Erion et al.   RNA

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

Riboswitches and the RNA World

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

The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure

(2009) Mona Ali et al.   JOURNAL OF MOLECULAR BIOLOGY

Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch

(2009) Nadia Kulshina et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of ligand binding by a c-di-GMP riboswitch

(2009) Kathryn D Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme

(2009) D. M. Shechner et al.   SCIENCE

Structural insights into amino acid binding and gene control by a lysine riboswitch

(2008) Alexander Serganov et al.   NATURE

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

Structural inference of native and partially folded RNA by high-throughput contact mapping

(2008) R. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

The Complete VS Ribozyme in Solution Studied by Small-Angle X-Ray Scattering

(2008) Jan Lipfert et al.   STRUCTURE

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE