Related references
Note: Only part of the references are listed.Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations
Jianbo Zhao et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides
Vojtech Mlynsky et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Hfq-dependent mRNA unfolding promotes sRNA-based inhibition of translation
Mirthe Hoekzema et al.
EMBO JOURNAL (2019)
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions
Petra Kuhrova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations
Giulia Palermo et al.
JOURNAL OF STRUCTURAL BIOLOGY (2019)
Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM
Nina Ripin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Architectural principles for Hfq/Crc-mediated regulation of gene expression
Xue Yuan Pei et al.
ELIFE (2019)
The roles of structural dynamics in the cellular functions of RNAs
Laura R. Ganser et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)
Understanding the binding specificities of mRNA targets by the mammalian Quaking protein
Monika Sharma et al.
NUCLEIC ACIDS RESEARCH (2019)
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution
Karolina Maria Gorecka et al.
NATURE COMMUNICATIONS (2019)
Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations
Jure Borisek et al.
BIOMOLECULES (2019)
Translational regulation by bacterial small RNAs via an unusual Hfq-dependent mechanism
Muhammad S. Azam et al.
NUCLEIC ACIDS RESEARCH (2018)
Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa
Elisabeth Sonnleitner et al.
NUCLEIC ACIDS RESEARCH (2018)
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Jiri Sponer et al.
CHEMICAL REVIEWS (2018)
New developments in force fields for biomolecular simulations
Paul S. Nerenberg et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch
Miroslav Krepl et al.
NUCLEIC ACIDS RESEARCH (2018)
All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome
Lorenzo Casalino et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Hfq chaperone brings speed dating to bacterial sRNA
Andrew Santiago-Frangos et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2018)
Effects of protein-crystal hydration and temperature on side-chain conformational heterogeneity in monoclinic lysozyme crystals
Hakan Atakisi et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
Sandro Bottaro et al.
SCIENCE ADVANCES (2018)
The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs
Joanna Kwiatkowska et al.
RNA (2018)
How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?
Jiri Sponer et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2017)
Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition
Miroslav Krepl et al.
NUCLEIC ACIDS RESEARCH (2017)
Structural and dynamic properties of the C-terminal region of the Escherichia coli RNA chaperone Hfq: integrative experimental and computational studies
Bin Wen et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq
Eike C. Schulz et al.
SCIENTIFIC REPORTS (2017)
Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein
Monika Sharma et al.
SCIENTIFIC REPORTS (2017)
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kuhrova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective
Rafal Szabla et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs
Miroslav Krepl et al.
NUCLEIC ACIDS RESEARCH (2016)
C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA
Andrew Santiago-Frangos et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Structure of a low-population binding intermediate in protein-RNA recognition
Aditi N. Borkar et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
SMOG 2: A Versatile Software Package for Generating Structure-Based Models
Jeffrey K. Noel et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?
M. Krepl et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics
David E. Condon et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
Chad W. Hopkins et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq
Lijun Wang et al.
NUCLEIC ACIDS RESEARCH (2015)
The role of RNA conformation in RNA-protein recognition
Efrat Kligun et al.
RNA BIOLOGY (2015)
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
Christina Bergonzo et al.
RNA (2015)
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
Christina Bergonzo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Systematic Identification of Hypothetical Bacteriophage Proteins Targeting Key Protein Complexes of Pseudomonas aeruginosa
An Van den Bossche et al.
JOURNAL OF PROTEOME RESEARCH (2014)
Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching
Kirsten E. Robinson et al.
NUCLEIC ACIDS RESEARCH (2014)
Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa Carbon Catabolite Repression
Elisabeth Sonnleitner et al.
PLOS GENETICS (2014)
SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations
Scott Le Grand et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
Fang-Chieh Chou et al.
NATURE METHODS (2013)
The Pseudomonas aeruginosa Catabolite Repression Control Protein Crc Is Devoid of RNA Binding Activity
Tetyana Milojevic et al.
PLOS ONE (2013)
Cycling of RNAs on Hfq
E. Gerhart H. Wagner
RNA BIOLOGY (2013)
A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well
Gerrit M. Daubner et al.
EMBO JOURNAL (2012)
Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics
Pavel Banas et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract
Nicola Horstmann et al.
NUCLEIC ACIDS RESEARCH (2012)
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)
Hfq and its constellation of RNA
Joerg Vogel et al.
NATURE REVIEWS MICROBIOLOGY (2011)
RNAs actively cycle on the Sm-like protein Hfq
Aurelie Fender et al.
GENES & DEVELOPMENT (2010)
Classification and energetics of the base-phosphate interactions in RNA
Craig L. Zirbel et al.
NUCLEIC ACIDS RESEARCH (2009)
Structure of Escherichia coli Hfq bound to polyriboadenylate RNA
Todd M. Link et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa
E. Sonnleitner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
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)
Nature and magnitude of aromatic stacking of nucleic acid bases
Jiri Sponer et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
Jane S. Richardson et al.
RNA (2008)
Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures
Alexander Wlodawer et al.
FEBS JOURNAL (2008)
Hfq structure, function and ligand binding
Richard G. Brennan et al.
CURRENT OPINION IN MICROBIOLOGY (2007)
Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
J Sponer et al.
CHEMISTRY-A EUROPEAN JOURNAL (2006)
Translational autocontrol of the Escherichia coli hfq RNA chaperone gene
B Vecerek et al.
RNA (2005)
Structure of Pseudomonas aeruginosa Hfq protein
A Nikulin et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)
Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs
PJ Mikulecky et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)
Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein
MA Schumacher et al.
EMBO JOURNAL (2002)