Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution

Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1–40 Dimer Structures from Atomistic Simulations

(2016) Phuong H. Nguyen et al.   ACS Chemical Neuroscience

Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer’s Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies

(2016) Son Tung Ngo et al.   Journal of Chemical Information and Modeling

Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work

(2016) Son Tung Ngo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane-bound tetramer and trimer Aβ oligomeric species correlate with toxicity towards cultured neurons

(2016) Metta K. Jana et al.   JOURNAL OF NEUROCHEMISTRY

Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils

(2016) Michael T. Colvin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A2T and A2V Aβ peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure, and LTP inhibition

(2016) Brian Murray et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method

(2015) Son Tung Ngo et al.   Chemical Biology & Drug Design

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

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

The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models

(2015) Arun Kumar Somavarapu et al.   CHEMPHYSCHEM

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

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

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

Atomic-Level Study of the Effects of O4 Molecules on the Structural Properties of Protofibrillar Aβ Trimer: β-Sheet Stabilization, Salt Bridge Protection, and Binding Mechanism

(2015) Yunxiang Sun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling an In-Register, Parallel “Iowa” Aβ Fibril Structure Using Solid-State NMR Data from Labeled Samples with Rosetta

(2015) Nikolaos G. Sgourakis et al.   STRUCTURE

Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

(2015) Mookyung Cheon et al.   PLoS Computational Biology

Difference in dimer conformation between amyloid-β(1–42) and (1–43) proteins: Replica exchange molecular dynamics simulations in water

(2014) Atsushi Yano et al.   CHEMICAL PHYSICS LETTERS

Amyloid oligomer structure characterization from simulations: A general method

(2014) Phuong H. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

Effect of Taiwan Mutation (D7H) on Structures of Amyloid-β Peptides: Replica Exchange Molecular Dynamics Study

(2014) Phan Minh Truong et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fibril Elongation by Aβ17–42: Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations

(2014) Wei Han et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The molecular mechanism of fullerene-inhibited aggregation of Alzheimer's β-amyloid peptide fragment

(2014) Luogang Xie et al.   Nanoscale

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

Di-Tyrosine Cross-Link Decreases the Collisional Cross-Section of Aβ Peptide Dimers and Trimers in the Gas Phase: An Ion Mobility Study

(2014) Ewa Sitkiewicz et al.   PLoS One

Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of Aβ40 and Aβ42

(2013) Man Hoang Viet et al.   ACS Chemical Neuroscience

In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease

(2013) Pham Dinh Quoc Huy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Stable conformation of full-length amyloid-β (1–42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

(2013) Akisumi Okamoto et al.   CHEMICAL PHYSICS LETTERS

Molecular Mechanism of the Inhibition of EGCG on the Alzheimer Aβ1–42 Dimer

(2013) Tong Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer

(2013) Phuong H. Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

(2013) Abil E. Aliev et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations

(2012) Man Hoang Viet et al.   JOURNAL OF CHEMICAL PHYSICS

Curcumin Binds to Aβ1–40 Peptides and Fibrils Stronger Than Ibuprofen and Naproxen

(2012) Son Tung Ngo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structures of Aβ17–42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Top-leads from natural products for treatment of Alzheimer's disease: docking and molecular dynamics study

(2012) Son Tung Ngo et al.   MOLECULAR SIMULATION

Membrane and surface interactions of Alzheimer’s Aβ peptide - insights into the mechanism of cytotoxicity

(2011) Thomas L. Williams et al.   FEBS Journal

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

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

Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity

(2011) Man Hoang Viet et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A New Structural Model of Aβ40Fibrils

(2011) Ivano Bertini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils

(2011) Jan Bieschke et al.   Nature Chemical Biology

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

Association Thermodynamics and Conformational Stability of β-Sheet Amyloid β(17-42) Oligomers: Effects of E22Q (Dutch) Mutation and Charge Neutralization

(2010) Nikolay Blinov et al.   BIOPHYSICAL JOURNAL

Transmembrane Structures for Alzheimer’s Aβ1−42Oligomers

(2010) Birgit Strodel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein aggregation diseases: pathogenicity and therapeutic perspectives

(2010) Adriano Aguzzi et al.   NATURE REVIEWS DRUG DISCOVERY

Alzheimer's Disease

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

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

(2009) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Structure of the Amyloid-β (1−42) Monomer Absorbed To Model Phospholipid Bilayers: A Molecular Dynamics Study

(2009) Charles H. Davis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Dewetting and Hydrophobic Interaction in Physical and Biological Systems

(2008) Bruce J. Berne et al.   Annual Review of Physical Chemistry

The interaction of amyloid Aβ(1–40) with lipid bilayers and ganglioside as studied by 31P solid-state NMR

(2008) Yasumoto Nakazawa et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Computational Study on the Structural Diversity of Amyloid Beta Peptide (Aβ10-35) Oligomers

(2008) Soonmin Jang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A temperature predictor for parallel tempering simulations

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