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

Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

(2010) Hoang Bao Nam et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

(2010) Johnny C. Wu et al.   Journal of Chemical Theory and Computation

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

(2010) Nikolaos G. Sgourakis et al.   JOURNAL OF MOLECULAR BIOLOGY

Balance between α and β Structures in Ab Initio Protein Folding

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

Discrepancies between Conformational Distributions of a Polyalanine Peptide in Solution Obtained from Molecular Dynamics Force Fields and Amide I′ Band Profiles

(2010) Daniel Verbaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-β Fragment 29−42 by Replica Exchange Molecular Dynamics Simulations

(2010) Yan Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models

(2010) Mai Suan Li et al.   PHYSICAL REVIEW LETTERS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Force Field Bias in Protein Folding Simulations

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes

(2009) Dirk Matthes et al.   BIOPHYSICAL JOURNAL

Effect of β-sheet propensity on peptide aggregation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Diversity of kinetic pathways in amyloid fibril formation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

(2009) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Influence of Preformed Asp23−Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of Aβ Peptides with Implications for Rates of Fibril Formation

(2009) Govardhan Reddy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding simulations of three proteins having all α-helix, all β-strand and α/β-structures

(2009) Yoshitake Sakae et al.   MOLECULAR SIMULATION

Role of the Region 23-28 in Aβ Fibril Formation: Insights from Simulations of the Monomers and Dimers of Alzheimers Peptides Aβ40 and Aβ42

(2008) Adrien Melquiond et al.   Current Alzheimer Research

The Role of Metals in β -Amyloid Peptide Aggregation: X-Ray Spectroscopy and Numerical Simulations

(2008) S. Morante   Current Alzheimer Research

Energy landscapes of the monomer and dimer of the Alzheimer’s peptide Aβ(1–28)

(2008) Xiao Dong et al.   JOURNAL OF CHEMICAL PHYSICS

Probing the mechanisms of fibril formation using lattice models

(2008) Mai Suan Li et al.   JOURNAL OF CHEMICAL PHYSICS

Alanine Polypeptide Structural Fingerprints at Room Temperature: What Can Be Gained from Non-Harmonic Car−Parrinello Molecular Dynamics Simulations

(2008) M.-P. Gaigeot   JOURNAL OF PHYSICAL CHEMISTRY A

Benchmarking Implicit Solvent Folding Simulations of the Amyloid β(10−35) Fragment†

(2008) Andrew Kent et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

(2008) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A temperature predictor for parallel tempering simulations

(2008) Alexandra Patriksson et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

(2008) Yan Lu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Targeting the early steps of Aβ16-22 protofibril disassembly by N-methylated inhibitors: A numerical study

(2008) Yassmine Chebaro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protofibril Assemblies of the Arctic, Dutch, and Flemish Mutants of the Alzheimer's Aβ1–40 Peptide

(2007) Nicolas Lux Fawzi et al.   BIOPHYSICAL JOURNAL