RNA Chaperones and the RNA Folding Problem
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September 1995 |
Constant pressure molecular dynamics for molecular systems
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December 1983 |
Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena
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November 1982 |
Folding of RNA involves parallel pathways
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October 1997 |
A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops
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December 1996 |
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
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January 2006 |
Free-energy landscape of a hyperstable RNA tetraloop
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May 2016 |
RNA folding pathways in stop motion
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April 2016 |
Exposing the kinetic traps in RNA folding
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journal
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June 1999 |
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
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journal
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September 2016 |
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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journal
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February 2008 |
RNA force field with accuracy comparable to state-of-the-art protein force fields
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January 2018 |
Recognition of Planar and Nonplanar Ligands in the Malachite Green-RNA Aptamer Complex
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December 2003 |
Isolation of new ribozymes from a large pool of random sequences [see comment]
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September 1993 |
How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?: Atomistic molecular dynamics simulations of RNA and protein-RNA complexes
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November 2016 |
Mapping the Universe of RNA Tetraloop Folds
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July 2017 |
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".
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November 1990 |
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
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June 2015 |
Tertiary Motifs in RNA Structure and Folding
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August 1999 |
Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study
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February 2010 |
Promoting transparency and reproducibility in enhanced molecular simulations
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July 2019 |
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
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March 1994 |
Exceptionally Stable Nucleic Acid Hairpins
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June 1995 |
Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides
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May 2020 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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journal
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April 1998 |
Native contacts determine protein folding mechanisms in atomistic simulations
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October 2013 |
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions
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journal
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March 2019 |
Structural Motifs in RNA
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journal
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June 1999 |
Structural Insight into RNA Hairpin Folding Intermediates
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July 2008 |
PLUMED 2: New feathers for an old bird
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February 2014 |
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
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journal
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March 2010 |
Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing
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September 1996 |
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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journal
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May 1995 |
Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
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May 2016 |
Direct Revelation of Multiple Conformations in RNA by Femtosecond Dynamics
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April 2007 |
Exploring the Energy Landscape of a Small RNA Hairpin
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February 2006 |
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.
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March 1988 |
Insights into RNA structure and function from genome-wide studies
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May 2014 |
Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
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October 2006 |
A molecular dynamics method for simulations in the canonical ensemble
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June 1984 |
Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops
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July 1991 |
Loop and stem dynamics during RNA hairpin folding and unfolding
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October 2010 |
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
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September 2013 |
GROMACS: A message-passing parallel molecular dynamics implementation
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September 1995 |
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
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journal
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May 2018 |
Structures, Kinetics, Thermodynamics, and Biological Functions of RNA Hairpins
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May 2008 |
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
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journal
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January 2008 |
Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics
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July 2015 |
Quality Threshold Clustering of Molecular Dynamics: A Word of Caution
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September 2019 |
The molecular configuration of deoxyribonucleic acid
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April 1960 |
Enhanced Sampling in the Well-Tempered Ensemble
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May 2010 |
The Paradoxical Behavior of a Highly Structured Misfolded Intermediate in RNA Folding
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October 2006 |
Dynamics of the RNA Hairpin GNRA Tetraloop †
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journal
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April 2000 |
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
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August 2016 |
Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations
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January 2012 |
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
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June 2007 |
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
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November 2010 |
Folding intermediates of a self-splicing RNA: mispairing of the catalytic core
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July 1998 |
Polymorphic transitions in single crystals: A new molecular dynamics method
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December 1981 |
Integrating NMR and simulations reveals motions in the UUCG tetraloop
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May 2020 |
Fitting Corrections to an RNA Force Field Using Experimental Data
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April 2019 |
Balance between α and β Structures in Ab Initio Protein Folding
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June 2010 |
A Time-Independent Free Energy Estimator for Metadynamics
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July 2014 |
Canonical dynamics: Equilibrium phase-space distributions
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March 1985 |
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
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August 2011 |
Geometric deep learning of RNA structure
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August 2021 |
Visualizing transient low-populated structures of RNA
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October 2012 |
Computer Folding of RNA Tetraloops? Are We There Yet?
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March 2013 |
Peptide Folding: When Simulation Meets Experiment
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January 1999 |
RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop 1 1Edited by J. Dovdna
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April 2002 |
Thermodynamics of DNA Hybridization from Atomistic Simulations
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January 2021 |
A smooth particle mesh Ewald method
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November 1995 |
The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models
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April 2019 |
The Ribosome Is a Ribozyme
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August 2000 |
Revised AMBER Parameters for Bioorganic Phosphates
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October 2012 |
Escaping free-energy minima
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journal
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September 2002 |
Hierarchy and Dynamics of rna Folding
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June 1997 |
A boundary correction algorithm for metadynamics in multiple dimensions
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August 2013 |
Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
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February 2015 |
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
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April 2015 |