How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Extension of the AMBER molecular dynamics software to Intel’s Many Integrated Core (MIC) architecture

(2016) Perri J. Needham et al.   COMPUTER PHYSICS COMMUNICATIONS

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

(2016) Petra Kührová et al.   Journal of Chemical Theory and Computation

Empirical Corrections to the Amber RNA Force Field with Target Metadynamics

(2016) Alejandro Gil-Ley et al.   Journal of Chemical Theory and Computation

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

Disagreement Between the Structure of the dTpT Thymine Pair Determined by NMR and Molecular Dynamics Simulations Using Amber 14 Force Fields

(2016) Collins Nganou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA folding pathways in stop motion

(2016) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

(2016) Miroslav Krepl et al.   NUCLEIC ACIDS RESEARCH

Free-energy landscape of a hyperstable RNA tetraloop

(2016) Jacob C. Miner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

(2016) Tai-Sung Lee et al.   ACS Catalysis

Determination of hepatitis delta virus ribozyme N(–1) nucleobase and functional group specificity using internal competition kinetics

(2015) Daniel L. Kellerman et al.   ANALYTICAL BIOCHEMISTRY

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

(2015) Francesco Di Palma et al.   BMC BIOINFORMATICS

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

(2015) Susanta Haldar et al.   Journal of Chemical Theory and Computation

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?

(2015) M. Krepl et al.   Journal of Chemical Theory and Computation

Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations

(2015) Michael V. Schrodt et al.   Journal of Chemical Theory and Computation

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

(2015) Reid F. Brown et al.   Journal of Chemical Theory and Computation

Improved Force Field Parameters Lead to a Better Description of RNA Structure

(2015) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

(2015) David E. Condon et al.   Journal of Chemical Theory and Computation

Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

(2015) Holger Kruse et al.   Journal of Chemical Theory and Computation

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

(2015) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

(2015) Marek Havrila et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

(2015) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

(2015) Kamali N. Sripathi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

(2015) Nikita Vasilyev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM

(2015) Brian K. Radak et al.   RNA

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

(2015) George M. Giambaşu et al.   RNA

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

(2015) Christina Bergonzo et al.   RNA

QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches

(2014) Holger Kruse et al.   Journal of Chemical Theory and Computation

Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations

(2014) Da-Wei Li et al.   Journal of Chemical Theory and Computation

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

(2014) Konstantinos Gkionis et al.   Journal of Chemical Theory and Computation

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

(2014) Daniel R. Roe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

(2014) Jiří Šponer et al.   Journal of Physical Chemistry Letters

Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA

(2014) Francesco Musiani et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins

(2014) Debayan Chakraborty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage

(2014) Gary J. Kapral et al.   NUCLEIC ACIDS RESEARCH

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

(2014) K. N. Sripathi et al.   RNA

An introduction to recurrent nucleotide interactions in RNA

(2014) Blake A. Sweeney et al.   Wiley Interdisciplinary Reviews-RNA

Identification of the Catalytic Mg2+ Ion in the Hepatitis Delta Virus Ribozyme

(2013) Ji Chen et al.   BIOCHEMISTRY

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Simulating movement of tRNA through the ribosome during hybrid-state formation

(2013) Paul C. Whitford et al.   JOURNAL OF CHEMICAL PHYSICS

Computer Folding of RNA Tetraloops? Are We There Yet?

(2013) Petra Kührová et al.   Journal of Chemical Theory and Computation

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

(2013) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

(2013) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

(2013) Niel M. Henriksen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin–Ricin Internal Loop

(2013) Marek Havrila et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loop-loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

(2013) O. Allner et al.   RNA

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch

(2013) F. Di Palma et al.   RNA

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

Revised AMBER Parameters for Bioorganic Phosphates

(2012) T. Steinbrecher et al.   Journal of Chemical Theory and Computation

Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study

(2012) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and mechanical properties of the ribosomal L1 stalk three-way junction

(2012) Kamila Réblová et al.   NUCLEIC ACIDS RESEARCH

End-to-end attraction of duplex DNA

(2012) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Charged Nucleobases and Their Potential for RNA Catalysis

(2011) Jennifer L. Wilcox et al.   ACCOUNTS OF CHEMICAL RESEARCH

Metal Binding Motif in the Active Site of the HDV Ribozyme Binds Divalent and Monovalent Ions

(2011) Narayanan Veeraraghavan et al.   BIOCHEMISTRY

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions

(2011) Ilyas Yildirim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation

(2011) Narayanan Veeraraghavan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path

(2011) Tai-Sung Lee et al.   Journal of Physical Chemistry Letters

Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction

(2011) Anh Tuân Phan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch

(2011) U. Doshi et al.   RNA

A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

(2010) Jui-Hui Chen et al.   BIOCHEMISTRY

Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study

(2010) Nan-Jie Deng et al.   BIOPHYSICAL JOURNAL

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

Long-Distance Communication in the HDV Ribozyme: Insights from Molecular Dynamics and Experiments

(2010) Narayanan Veeraraghavan et al.   JOURNAL OF MOLECULAR BIOLOGY

Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics

(2010) Guanghong Zuo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protonation States of the Key Active Site Residues and Structural Dynamics of theglmSRiboswitch As Revealed by Molecular Dynamics

(2010) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

(2010) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

(2010) A. J. DePaul et al.   NUCLEIC ACIDS RESEARCH

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

(2009) Mark A. Ditzler et al.   ACCOUNTS OF CHEMICAL RESEARCH

Fast Folding of an RNA Tetraloop on a Rugged Energy Landscape Detected by a Stacking-Sensitive Probe

(2009) Krishnarjun Sarkar et al.   BIOPHYSICAL JOURNAL

Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis

(2009) Laura Riccardi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

(2009) Pavel Banáš et al.   METHODS

Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch

(2009) J. M. Kelley et al.   NUCLEIC ACIDS RESEARCH

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

(2009) A. Villa et al.   NUCLEIC ACIDS RESEARCH

Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM

(2009) Kamila Réblová et al.   NUCLEIC ACIDS RESEARCH

General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

(2008) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Insight into RNA Hairpin Folding Intermediates

(2008) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A short guide for molecular dynamics simulations of RNA systems

(2008) Yaser Hashem et al.   METHODS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg

(2007) Alessandra Villa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin

(2007) Angel E. Garcia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY