Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics (original) (raw)

Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins

Kai Kohlhoff

Structure, 2010

View PDFchevron_right

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

Michele Vendruscolo, Jesper Ferkinghoff-borg, Wouter Boomsma

Proceedings of the National Academy of Sciences of the United States of America, 2014

View PDFchevron_right

Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins

Xavier Salvatella

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2012

View PDFchevron_right

Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology

Xavier Salvatella

2009

View PDFchevron_right

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

Victor Muñoz

Journal of the American Chemical Society, 2015

View PDFchevron_right

Exploration of Protein Conformational Change with PELE and Meta-Dynamics

ali Shah Hosseini

Journal of Chemical Theory and Computation, 2012

View PDFchevron_right

Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation

Józef Lewandowski, Maria Baias

View PDFchevron_right

New Tools Provide New Insights in NMR Studies of Protein Dynamics

Anthony Mittermaier

Science, 2006

View PDFchevron_right

Atomic-Level Characterization of the Structural Dynamics of Proteins

Stefano Piana

Science, 2010

View PDFchevron_right

Molecular dynamics simulations to study protein folding and unfolding

Amedeo Caflisch

Protein Science Encyclopedia, 2005

View PDFchevron_right

Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding

Guido Tiana

The Journal of Chemical Physics, 2012

View PDFchevron_right

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

Stefano Piana

Current Opinion in Structural Biology, 2014

View PDFchevron_right

Molecular Dynamics Simulations of Proteins and Peptides: From Folding to Drug Design

paul tavan

Current Protein & Peptide Science, 2008

View PDFchevron_right

Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate

P. Schanda, Isabel Ayala

Journal of the American Chemical Society, 2012

View PDFchevron_right

The refinement of NMR structures by molecular dynamics simulation

Andrew Torda

Computer Physics Communications, 1991

View PDFchevron_right

Advances in free-energy-based simulations of protein folding and ligand binding

Alberto Perez

Current opinion in structural biology, 2016

View PDFchevron_right

Molecular Dynamics Simulation of Proteins: A Brief Overview

Sachin Patodia

Journal of Physical Chemistry & Biophysics, 2014

View PDFchevron_right

Kurt Wüthrich, the ETH Zürich, and the Development of NMR Spectroscopy for the Investigation of Structure, Dynamics, and Folding of Proteins

Harald Schwalbe

ChemBioChem, 2003

View PDFchevron_right

NMR Methods of Characterizing Biomolecular Structural Dynamics and Conformational Ensembles

David Boehr

Methods, 2018

View PDFchevron_right

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

Karl Freed

View PDFchevron_right

From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A

Sebastian Kmiecik

The Journal of Physical Chemistry B, 2012

View PDFchevron_right

Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data

David Wales

Journal of Chemical Theory and Computation

View PDFchevron_right

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

Diwakar shukla

Current Opinion in Structural Biology, 2013

View PDFchevron_right

Conformational Ensemble Calculations: Analysis of Protein and Nucleic Acid NMR Data

Todd M Billeci

Biological Magnetic Resonance: Structure, Computation and Dynamics in Protein NMR, 1999

View PDFchevron_right

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation

Hiqmet Kamberaj

View PDFchevron_right

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

Adam Liwo

Proceedings of The National Academy of Sciences, 2005

View PDFchevron_right

Molecular dynamics simulation of protein

Sachin Patodia

View PDFchevron_right

Describing protein folding kinetics by molecular dynamics simulations

Chris T J C Ward

2004

View PDFchevron_right

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

Adam Liwo

Annual Review of Physical Chemistry, 2007

View PDFchevron_right

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

Ellinor Haglund

The Journal of chemical physics, 2015

View PDFchevron_right

Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements

Vijay Pande

View PDFchevron_right

All-atom molecular dynamics simulations using orientational constraints from anisotropic NMR samples

Ulrich Sternberg

Journal of Biomolecular NMR, 2007

View PDFchevron_right

Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

Cezary Czaplewski

The Journal of Physical Chemistry a, 2010

View PDFchevron_right

A free-energy approach for all-atom protein simulation

Abhinav Verma

2009

View PDFchevron_right

Molecular Dynamics Simulations of Protein Folding

Angel Garcia

Protein Structure Prediction, 2008

View PDFchevron_right