Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop

(2017) Aditi N. Borkar et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering

(2016) Vincenzo Venditti et al.   CHEMICAL REVIEWS

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

(2016) Elena Papaleo et al.   CHEMICAL REVIEWS

A structural ensemble of a ribosome–nascent chain complex during cotranslational protein folding

(2016) Lisa D Cabrita et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A critical assessment of methods to recover information from averaged data

(2016) Enrico Ravera et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structure of a low-population binding intermediate in protein-RNA recognition

(2016) Aditi N. Borkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A structural ensemble of a ribosome–nascent chain complex during cotranslational protein folding

(2016) Lisa D Cabrita et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

(2016) Massimiliano Bonomi et al.   Scientific Reports

Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors

(2015) Sigrid Milles et al.   CELL

Dynamic properties of force fields

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

A Rigorous and Efficient Method To Reweight Very Large Conformational Ensembles Using Average Experimental Data and To Determine Their Relative Information Content

(2015) Hoi Tik Alvin Leung et al.   Journal of Chemical Theory and Computation

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

(2015) Jim Pfaendtner et al.   Journal of Chemical Theory and Computation

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

(2015) Sarah Rauscher 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

Comparing Molecular Dynamics Force Fields in the Essential Subspace

(2015) Fernando Martín-García et al.   PLoS One

Introducing Protein Intrinsic Disorder

(2014) Johnny Habchi et al.   CHEMICAL REVIEWS

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

(2014) Ferruccio Palazzesi et al.   Journal of Chemical Theory and Computation

A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings

(2014) Carlo Camilloni et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistical Mechanics of the Denatured State of a Protein Using Replica-Averaged Metadynamics

(2014) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Conformational Populations and Functionally Relevant Substates

(2013) Arvind Ramanathan et al.   ACCOUNTS OF CHEMICAL RESEARCH

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

(2013) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

(2013) Andrea Cavalli et al.   JOURNAL OF CHEMICAL PHYSICS

Replica-Averaged Metadynamics

(2013) Carlo Camilloni et al.   Journal of Chemical Theory and Computation

Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data

(2013) Sandro Bottaro et al.   Journal of Chemical Theory and Computation

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties

(2013) Christian L. Wennberg et al.   Journal of Chemical Theory and Computation

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts

(2012) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances

(2009) Kai J. Kohlhoff et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation