Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

CHARMM TIP3P Water Model Suppresses Peptide Folding by Solvating the Unfolded State

(2016) Sander Boonstra et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Advances in the Simulation of Protein Aggregation at the Atomistic Scale

(2016) Martín Carballo-Pacheco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2016) Jing Huang et al.   NATURE METHODS

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

(2015) Jessica Nasica-Labouze et al.   CHEMICAL REVIEWS

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

Structures of the Alzheimer’s Wild-Type Aβ1-40 Dimer from Atomistic Simulations

(2015) Bogdan Tarus et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations

(2015) Gül H. Zerze et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Regulation and aggregation of intrinsically disordered peptides

(2015) Zachary A. Levine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aβ and cognitive change: Examining the preclinical and prodromal stages of Alzheimer's disease

(2014) Yen Ying Lim et al.   Alzheimers & Dementia

YASARA View—molecular graphics for all devices—from smartphones to workstations

(2014) Elmar Krieger et al.   BIOINFORMATICS

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

Neurological update: dementia

(2014) A. J. Larner   JOURNAL OF NEUROLOGY

The amyloid state and its association with protein misfolding diseases

(2014) Tuomas P. J. Knowles et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Temperature-dependent solvation modulates the dimensions of disordered proteins

(2014) R. Wuttke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsically Disordered Proteins: Where Computation Meets Experiment

(2014) Virginia Burger et al.   Polymers

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Protein Misfolding in Disease and Small Molecule Therapies

(2013) Claudio M. Gomes   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Molecular Mechanism of Misfolding and Aggregation of Aβ(13–23)

(2013) Sándor Lovas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy of Solvated Salt Bridges: A Simulation and Experimental Study

(2013) Andrew D. White et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Role of β-Hairpin Formation in Aggregation: The Self-Assembly of the Amyloid-β(25–35) Peptide

(2012) Luca Larini et al.   BIOPHYSICAL JOURNAL

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Systematic Validation of Protein Force Fields against Experimental Data

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

Role of Water in Protein Aggregation and Amyloid Polymorphism

(2011) D. Thirumalai et al.   ACCOUNTS OF CHEMICAL RESEARCH

A partially folded structure of amyloid-beta(1–40) in an aqueous environment

(2011) Subramanian Vivekanandan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Single-Molecule Atomic Force Microscopy Force Spectroscopy Study of Aβ-40 Interactions

(2011) Bo-Hyun Kim et al.   BIOCHEMISTRY

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

(2011) Song-Ho Chong et al.   JOURNAL OF CHEMICAL PHYSICS

Cerebral Amyloid Angiopathy: A Systematic Review

(2011) Alessandro Biffi et al.   Journal of Clinical Neurology

Ion Mobility Separation Coupled with MS Detects Two Structural States of Alzheimer's Disease Aβ1–40 Peptide Oligomers

(2011) Marcin Kłoniecki et al.   JOURNAL OF MOLECULAR BIOLOGY

Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization

(2011) Dirk Matthes et al.   PLoS One

Soluble amyloid  -protein dimers isolated from Alzheimer cortex directly induce Tau hyperphosphorylation and neuritic degeneration

(2011) M. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

(2010) Tsuyoshi Terakawa et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Review: Sporadic cerebral amyloid angiopathy

(2010) J. Attems et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Alzheimer's Disease

(2010) Henry W. Querfurth et al.   NEW ENGLAND JOURNAL OF MEDICINE

Structural Characterization of a Soluble Amyloid β-Peptide Oligomer

(2009) Liping Yu et al.   BIOCHEMISTRY

Fever in the critically ill medical patient

(2009) Kevin B. Laupland   CRITICAL CARE MEDICINE

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease

(2009) Summer L. Bernstein et al.   Nature Chemistry

Structure-neurotoxicity relationships of amyloid  -protein oligomers

(2009) K. Ono et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide

(2009) X. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A temperature predictor for parallel tempering simulations

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