The combined force field-sampling problem in simulations of disordered amyloid-β peptides

Highly Disordered Amyloid- β Monomer Probed by Single-Molecule FRET and MD Simulation

(2018) Fanjie Meng et al.   BIOPHYSICAL JOURNAL

New developments in force fields for biomolecular simulations

(2018) Paul S Nerenberg et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations

(2018) Alan Hicks et al.   JOURNAL OF CHEMICAL PHYSICS

Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins

(2018) Taylor Firman et al.   JOURNAL OF CHEMICAL PHYSICS

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

(2018) Gustavo Fuertes et al.   SCIENCE

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

(2018) Joshua A. Riback et al.   SCIENCE

Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

(2018) Robert B. Best et al.   SCIENCE

Theory, simulations, and experiments show that proteins fold by multiple pathways

(2017) William A. Eaton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements

(2017) Gustavo Fuertes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

(2017) Joshua A. Riback et al.   SCIENCE

Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

(2017) Christopher M. Siwy et al.   PLoS Computational Biology

Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

(2016) Julien Roche et al.   BIOCHEMISTRY

Molecular dynamics studies of a β-sheet blocking peptide with the full-length amyloid beta peptide of Alzheimer’s disease

(2016) Zohreh Amini et al.   CANADIAN JOURNAL OF CHEMISTRY

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

(2016) James Lincoff et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models

(2016) João Henriques et al.   Journal of Chemical Theory and Computation

Finding Our Way in the Dark Proteome

(2016) Asmit Bhowmick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins

(2016) David H. Brookes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS

(2016) Mikayel Aznauryan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations

(2015) Wenwei Zheng 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

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

(2015) João Henriques et al.   Journal of Chemical Theory and Computation

Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations

(2015) Trang Nhu Do et al.   Journal of Chemical Theory and Computation

Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields

(2015) David J. Rosenman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Varied Probability of Staying Collapsed/Extended at the Conformational Equilibrium of Monomeric Aβ40 and Aβ42

(2015) Wanling Song et al.   Scientific Reports

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

(2015) Daniele Granata et al.   Scientific Reports

Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of Aβ40 and Aβ42

(2014) Man Hoang Viet et al.   ACS Chemical Neuroscience

The C-Terminal Threonine of Aβ43 Nucleates Toxic Aggregation via Structural and Dynamical Changes in Monomers and Protofibrils

(2014) Alexander E. Conicella et al.   BIOCHEMISTRY

New Force Field on Modeling Intrinsically Disordered Proteins

(2014) Wei Wang et al.   Chemical Biology & Drug Design

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

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Comparison of Structure Determination Methods for Intrinsically Disordered Amyloid-β Peptides

(2014) K. Aurelia Ball et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins

(2014) Ignacia Echeverria et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Differences in β-strand Populations of Monomeric Aβ40 and Aβ42

(2013) K. Aurelia Ball et al.   BIOPHYSICAL JOURNAL

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

(2013) Cameron Abrams et al.   Entropy

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

(2013) David J. Rosenman et al.   JOURNAL OF MOLECULAR BIOLOGY

Characterization of disordered proteins with ENSEMBLE

(2012) Mickaël Krzeminski et al.   BIOINFORMATICS

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

(2012) Yu-Shan Lin et al.   BIOPHYSICAL JOURNAL

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies

(2012) Paul S. Nerenberg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

(2012) A. Soranno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy

(2012) H. Hofmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides

(2011) K. Aurelia Ball et al.   BIOCHEMISTRY

SHIFTX2: significantly improved protein chemical shift prediction

(2011) Beomsoo Han et al.   JOURNAL OF BIOMOLECULAR NMR

Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

(2011) Paul S. Nerenberg et al.   Journal of Chemical Theory and Computation

Influence of water–protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

(2011) Dietmar Paschek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer

(2011) Phuong H. Nguyen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ensemble modeling of protein disordered states: Experimental restraint contributions and validation

(2011) Joseph A. Marsh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

(2010) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

(2010) Robert B. Best et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Function and structure of inherently disordered proteins

(2008) A Keith Dunker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach

(2008) Hugh Nymeyer   Journal of Chemical Theory and Computation

Structure and Dynamics of the Aβ21–30Peptide from the Interplay of NMR Experiments and Molecular Simulations

(2008) Nicolas L. Fawzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY