Related references
Note: Only part of the references are listed.Atomic-Level Characterization of the Ensemble of the Aβ(1-42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms
Nikolaos G. Sgourakis et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
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
Yan Lu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations
Hoang Bao Nam et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field
Johnny C. Wu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Balance between a and β Structures in Ab Initio Protein Folding
Robert B. Best et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Discrepancies between Conformational Distributions of a Polyalanine Peptide in Solution Obtained from Molecular Dynamics Force Fields and Amide I′ Band Profiles
Daniel Verbaro et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study
B. Urbanc et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Folding simulations of three proteins having all alpha-helix, all beta-strand and alpha/beta-structures
Yoshitake Sakae et al.
MOLECULAR SIMULATION (2010)
Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models
Mai Suan Li et al.
PHYSICAL REVIEW LETTERS (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
Force Field Bias in Protein Folding Simulations
Peter L. Freddolino et al.
BIOPHYSICAL JOURNAL (2009)
Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes
Dirk Matthes et al.
BIOPHYSICAL JOURNAL (2009)
Effect of β-sheet propensity on peptide aggregation
Giovanni Bellesia et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Diversity of kinetic pathways in amyloid fibril formation
Giovanni Bellesia et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent
Yassmine Chebaro et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
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
Yassmine Chebaro et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
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
Govardhan Reddy et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides
Robert B. Best et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
Yan Lu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Targeting the early steps of A beta 16-22 protofibril disassembly by N-methylated inhibitors: A numerical study
Yassmine Chebaro et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Protofibril assemblies of the arctic, dutch, and flemish mutants of the Alzheimer's Aβ1-40 peptide
Nicolas Lux Fawzi et al.
BIOPHYSICAL JOURNAL (2008)
Role of the region 23-28 in Aβ fibril formation:: Insights from simulations of the monomers and dimers of Alzheimer's peptides Aβ40 and Aβ42
Adrien Melquiond et al.
CURRENT ALZHEIMER RESEARCH (2008)
The Role of Metals in β-Amyloid Peptide Aggregation: X-Ray Spectroscopy and Numerical Simulations
S. Morante
CURRENT ALZHEIMER RESEARCH (2008)
Energy landscapes of the monomer and dimer of the Alzheimer's peptide Aβ(1-28)
Xiao Dong et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Probing the mechanisms of fibril formation using lattice models
Mai Suan Li et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Alanine Polypeptide Structural Fingerprints at Room Temperature: What Can Be Gained from Non-Harmonic Car-Parrinello Molecular Dynamics Simulations
M. -P. Gaigeot
JOURNAL OF PHYSICAL CHEMISTRY A (2008)
Benchmarking implicit solvent folding simulations of the amyloid β(10-35) fragment
Andrew Kent et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
A temperature predictor for parallel tempering simulations
Alexandra Patriksson et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
New insights into the mechanism of Alzheimer amyloid-β fibrillogenesis inhibition by N-methylated peptides
Patricia Soto et al.
BIOPHYSICAL JOURNAL (2007)
Automated 2D IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide
Sang-Hee Shim et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
The Alzheimer's peptides Aβ40 and 42 adopt distinct conformations in water:: A combined MD/NMR study
Nikolaos G. Sgourakis et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Dissociation of Aβ16-22 amyloid fibrils probed by molecular dynamics
Takako Takeda et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Coarse-grained protein molecular dynamics simulations
Philippe Derreumaux et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism
Phuong H. Nguyen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Computational Simulations of the Early Steps of Protein Aggregation
Guanghong Wei et al.
PRION (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Stability and structure of oligomers of the Alzheimer peptide Aβ16-22:: From the dimer to the 32-mer
Ute F. Rohrig et al.
BIOPHYSICAL JOURNAL (2006)
Impact of the mutation A21G (Flemish variant) on Alzheimer's β-amyloid dimers by molecular dynamics simulations
Alexis Huet et al.
BIOPHYSICAL JOURNAL (2006)
Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
Buyong Ma et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2006)
Interpreting the aggregation kinetics of amyloid peptides
Riccardo Pellarin et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Atomic-level description of amyloid β-dimer formation
S Gnanakaran et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
3D structure of Alzheimer's amyloid-β(1-42) fibrils
T Lührs et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments
NV Buchete et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates
SA Petty et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Structure of the cross-β spine of amyloid-like fibrils
R Nelson et al.
NATURE (2005)
Helix-coil transition of alanine peptides in water:: Force field dependence on the folded and unfolded structures
S Gnanakaran et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
YG Mu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Comparisons of force fields for proteins by generalized-ensemble simulations
T Yoda et al.
CHEMICAL PHYSICS LETTERS (2004)
Characterization of non-alpha helical conformations in Ala peptides
AE Garcia
POLYMER (2004)
In silico assembly of Alzheimer's Aβ16-22 peptide into β-sheets
S Santini et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
In silico study of amyloid β-protein folding and oligomerization
B Urbanc et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Molecular pathways to neurodegeneration
E Bossy-Wetzel et al.
NATURE MEDICINE (2004)
Pathway complexity of Alzheimer's β-amyloid Aβ16-22 peptide assembly
S Santini et al.
STRUCTURE (2004)
Protein aggregation and neurodegenerative disease
CA Ross et al.
NATURE MEDICINE (2004)
Oligomerization of amyloid Aβ16-22 peptides using hydrogen bonds and hydrophobicity forces
G Favrin et al.
BIOPHYSICAL JOURNAL (2004)
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
HD Nguyen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Validation of an all-atom protein force field: From dipeptides to larger peptides
S Gnanakaran et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Rationalization of the effects of mutations on peptide and protein aggregation rates
F Chiti et al.
NATURE (2003)
Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments
YG Mu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
The role of side-chain interactions in the early steps of aggregation:: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
J Gsponer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Dissecting the assembly of Aβ16-22 amyloid peptides into antiparallel β sheets
DK Klimov et al.
STRUCTURE (2003)
A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR
AT Petkova et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases
F Chiti et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics
RI Dima et al.
PROTEIN SCIENCE (2002)
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)
Prediction of amyloid fibril-forming proteins
Y Kallberg et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Conformational propagation with prion-like characteristics in a simple model of protein folding
PM Harrison et al.
PROTEIN SCIENCE (2001)
GROMACS 3.0: a package for molecular simulation and trajectory analysis
E Lindahl et al.
JOURNAL OF MOLECULAR MODELING (2001)
Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of β-sheets in Alzheimer's β-amyloid fibrils
ON Antzutkin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)
Amyloid fibril formation by Aβ16-22, a seven-residue fragment of the Alzheimer's β-amyloid peptide, and structural characterization by solid state NMR
JJ Balbach et al.
BIOCHEMISTRY (2000)
Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: A structural clue to amyloid assembly
DE Otzen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)
The protofilament substructure of amyloid fibrils
LC Serpell et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Amyloid fibrillogenesis: themes and variations
JC Rochet et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2000)