The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models

IMPROVING THE PERFORMANCE OF THE AMBER RNA FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

(2019) Petra Kührová et al.   Journal of Chemical Theory and Computation

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Exploring RNA structure and dynamics through enhanced sampling simulations

(2018) Vojtěch Mlýnský et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computing the Free Energy without Collective Variables

(2018) Alex Rodriguez et al.   Journal of Chemical Theory and Computation

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

(2018) Sandro Bottaro et al.   Science Advances

Barnaba: software for analysis of nucleic acid structures and trajectories

(2018) Sandro Bottaro et al.   RNA

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

(2018) Pablo D. Dans et al.   Chem

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models

(2017) Giovanni Pinamonti et al.   Journal of Chemical Theory and Computation

Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

(2017) Nuria Plattner et al.   Nature Chemistry

Unraveling Mg 2+ –RNA binding with atomistic molecular dynamics

(2017) Richard A. Cunha et al.   RNA

Physics-based all-atom modeling of RNA energetics and structure

(2017) Louis G. Smith et al.   Wiley Interdisciplinary Reviews-RNA

Estimating the intrinsic dimension of datasets by a minimal neighborhood information

(2017) Elena Facco et al.   Scientific Reports

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Density-based cluster algorithms for the identification of core sets

(2016) Oliver Lemke et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

(2016) Sandro Bottaro et al.   Journal of Physical Chemistry Letters

RNA folding pathways in stop motion

(2016) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

(2016) Lin-Tai Da et al.   Nature Communications

Advances in RNA molecular dynamics: a simulator's guide to RNA force fields

(2016) Sweta Vangaveti et al.   Wiley Interdisciplinary Reviews-RNA

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

Estimation and uncertainty of reversible Markov models

(2015) Benjamin Trendelkamp-Schroer et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé 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

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations

(2015) Shun Sakuraba et al.   Journal of Physical Chemistry Letters

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

(2015) Giovanni Pinamonti et al.   NUCLEIC ACIDS RESEARCH

Understanding the kinetic mechanism of RNA single base pair formation

(2015) Xiaojun Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Christina Bergonzo et al.   RNA

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

(2014) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

The role of nucleobase interactions in RNA structure and dynamics

(2014) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

(2014) Jordane Preto et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

(2013) Wei Huang et al.   PLoS Computational Biology

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

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

The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation

(2012) Aleksandar Spasic et al.   Journal of Chemical Theory and Computation

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

(2012) Ivana Beššeová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA Unwinding from Reweighted Pulling Simulations

(2012) Francesco Colizzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kinetic characterization of the critical step in HIV-1 protease maturation

(2012) S. K. Sadiq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Markov state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Real-Time Atomistic Description of DNA Unfolding

(2010) Alberto Perez et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Mechanism of RNA Double Helix-Propagation at Atomic Resolution†

(2009) Srividya Mohan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNA

(2009) Jasmin F. Sydow et al.   MOLECULAR CELL

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

The Dynamic Structural Basis of Differential Enhancement of Conformational Stability by 5′- and 3′-Dangling Ends in RNA†

(2008) John D. Liu et al.   BIOCHEMISTRY

The Pathway of Oligomeric DNA Melting Investigated by Molecular Dynamics Simulations

(2008) Ka-Yiu Wong et al.   BIOPHYSICAL JOURNAL

RNA dynamics: it is about time

(2008) Hashim M Al-Hashimi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B