Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide

The worldwide economic impact of dementia 2010

(2013) Anders Wimo et al.   Alzheimers & Dementia

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Differences in β-strand Populations of Monomeric Aβ40 and Aβ42

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

Structural Insights into Aβ42 Oligomers Using Site-directed Spin Labeling

(2013) Lei Gu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Structure and Dynamics of Small Soluble Aβ(1–40) Oligomers Studied by Top-Down Hydrogen Exchange Mass Spectrometry

(2012) Jingxi Pan et al.   BIOCHEMISTRY

Structures of the Amyloid β-Peptides Aβ1–40 and Aβ1–42 as Influenced by pH and a d-Peptide

(2012) Olujide O. Olubiyi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides

(2011) K. Aurelia Ball et al.   BIOCHEMISTRY

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Nature of the Amyloid-β Monomer and the Monomer-Oligomer Equilibrium

(2011) Suman Nag et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water

(2010) Chewook Lee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

(2009) Lauren Wickstrom 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

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Amyloid β-Protein Assembly and Alzheimer Disease

(2008) Robin Roychaudhuri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Amyloid β-Protein Monomer Folding: Free-Energy Surfaces Reveal Alloform-Specific Differences

(2008) Mingfeng Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

M35 Oxidation Induces Aβ40-like Structural and Dynamical Changes in Aβ42

(2008) Yilin Yan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2007) Berk Hess   Journal of Chemical Theory and Computation