Related references
Note: Only part of the references are listed.Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo
Oliver J. Melling et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)
Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias
Travis Hurst et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures
Jingyi Cao et al.
NUCLEIC ACIDS RESEARCH (2021)
Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure
Gregoire De Bisschop et al.
NON-CODING RNA (2021)
Electrochemistry, ion adsorption and dynamics in the double layer: a study of NaCl(aq) on graphite
Aaron R. Finney et al.
CHEMICAL SCIENCE (2021)
IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles
Afaf Saaidi et al.
NUCLEIC ACIDS RESEARCH (2020)
Machine learning a model for RNA structure prediction
Nicola Calonaci et al.
NAR GENOMICS AND BIOINFORMATICS (2020)
The interplay between molecular flexibility and RNA chemical probing reactivities analyzed at the nucleotide level via an extensive molecular dynamics study
Elisa Frezza et al.
METHODS (2019)
Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies
Steven Busan et al.
BIOCHEMISTRY (2019)
Barnaba: software for analysis of nucleic acid structures and trajectories
Sandro Bottaro et al.
RNA (2019)
ACPYPE update for nonuniform 1-4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS
Austen Bernardi et al.
SOFTWAREX (2019)
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Jiri Sponer et al.
CHEMICAL REVIEWS (2018)
Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis
Travis Hurst et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility
Vojtech Mlynsky et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2018)
Unraveling Mg2+-RNA binding with atomistic molecular dynamics
Richard A. Cunha et al.
RNA (2017)
SHAPE directed RNA folding
Ronny Lorenz et al.
BIOINFORMATICS (2016)
Cotranscriptional folding of a riboswitch at nucleotide resolution
Kyle E. Watters et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)
Cotranscriptional folding of a riboswitch at nucleotide resolution
Kyle E. Watters et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)
Molecular dynamics simulations of solutions at constant chemical potential
C. Perego et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
Giovanni Pinamonti et al.
NUCLEIC ACIDS RESEARCH (2015)
A Distinct, Sequence-Induced Conformation Is Required for Recognition of the Constitutive Decay Element RNA by Roquin
Luca Codutti et al.
STRUCTURE (2015)
Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids
Shu-ichi Nakano et al.
CHEMICAL REVIEWS (2014)
PLUMED 2: New feathers for an old bird
Gareth A. Tribello et al.
COMPUTER PHYSICS COMMUNICATIONS (2014)
Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations
Sirish Kaushik Lakkaraju et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Building Water Models: A Different Approach
Saeed Izadi et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
The role of nucleobase interactions in RNA structure and dynamics
Sandro Bottaro et al.
NUCLEIC ACIDS RESEARCH (2014)
RNA secondary structure modeling at consistent high accuracy using differential SHAPE
Greggory M. Rice et al.
RNA (2014)
Grand-Canonical-like Molecular-Dynamics Simulations by Using an Adaptive-Resolution Technique
Han Wang et al.
PHYSICAL REVIEW X (2013)
An RNA Mapping DataBase for curating RNA structure mapping experiments
Pablo Cordero et al.
BIOINFORMATICS (2012)
Exploring RNA Structural Codes with SHAPE Chemistry
Kevin M. Weeks et al.
ACCOUNTS OF CHEMICAL RESEARCH (2011)
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
Marie Zgarbova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Modeling and automation of sequencing-based characterization of RNA structure
Sharon Aviran et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Advances in RNA structure analysis by chemical probing
Kevin M. Weeks
CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
Pavel Banas et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
Allison J. DePaul et al.
NUCLEIC ACIDS RESEARCH (2010)
Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA
Mijeong Kang et al.
MOLECULAR CELL (2009)
Accurate SHAPE-directed RNA structure determination
Katherine E. Deigan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
In Suk Joung et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Refinenement of the AMBER force field for nucleic acids:: Improving the description of α/γ conformers
Alberto Perez et al.
BIOPHYSICAL JOURNAL (2007)
Breaking pseudo-twofold symmetry in the poliovirus 3′-UTR Y-stem by restoring Watson-Crick base pairs
Jan Zoll et al.
RNA (2007)
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
Stefanie A. Mortimer et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Automatic atom type and bond type perception in molecular mechanical calculations
Junmei Wang et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
Rebecca K. Montange et al.
NATURE (2006)
Selective 2 '-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution
Kevin A. Wilkinson et al.
NATURE PROTOCOLS (2006)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
EJ Merino et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Development and testing of a general amber force field
JM Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Structural insights into group II intron catalysis and branch-site selection
L Zhang et al.
SCIENCE (2002)
Geometric nomenclature and classification of RNA base pairs
NB Leontis et al.
RNA (2001)
Share Paper
