RNA folding pathways in stop motion

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

(2015) M. Krepl 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

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations

(2015) Andrea Pérez-Villa et al.   NUCLEIC ACIDS RESEARCH

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments

(2015) Giovanni Pinamonti et al.   NUCLEIC ACIDS RESEARCH

Mighty tiny

(2015) Kathleen B. Hall   RNA

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

(2015) Zhichao Miao 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

Native proteins trap high-energy transit conformations

(2015) A. E. Brereton et al.   Science Advances

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

(2014) Prashant S. Emani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

The role of nucleobase interactions in RNA structure and dynamics

(2014) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Invisible RNA state dynamically couples distant motifs

(2014) Janghyun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

(2013) Jason D. Tubbs et al.   BIOCHEMISTRY

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Computer Folding of RNA Tetraloops? Are We There Yet?

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

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

(2013) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

(2013) Paul C. Whitford et al.   PLoS Computational Biology

Computational approaches to RNA structure prediction, analysis, and design

(2011) Christian Laing et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Delineation of Folding Pathways of a β-Sheet Miniprotein

(2011) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

C-terminal domain of archaeal O -phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA Sec

(2010) R. Lynn Sherrer et al.   NUCLEIC ACIDS 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

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

(2009) M. Parisien et al.   RNA

A Probabilistic Model of RNA Conformational Space

(2009) Jes Frellsen et al.   PLoS Computational Biology

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE