The stability of cylindrin β-barrel amyloid oligomer models-A molecular dynamics study

Molecular Mechanisms of Amyloid Oligomers Toxicity

(2016) Rakez Kayed et al.   JOURNAL OF ALZHEIMERS DISEASE

Single Molecule Characterization of the Interactions between Amyloid-β Peptides and the Membranes of Hippocampal Cells

(2013) Priyanka Narayan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2012) Jingxi Pan et al.   BIOCHEMISTRY

Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation

(2012) Hlengisizwe Ndlovu et al.   BIOPHYSICAL JOURNAL

The Amyloid State of Proteins in Human Diseases

(2012) David Eisenberg et al.   CELL

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Structure and Dynamics of Amyloid-β Segmental Polymorphisms

(2012) Workalemahu M. Berhanu et al.   PLoS One

Out-of-register  -sheets suggest a pathway to toxic amyloid aggregates

(2012) C. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Side-chain hydrophobicity and the stability of Aβ16-22aggregates

(2012) Workalemahu M. Berhanu et al.   PROTEIN SCIENCE

Atomic View of a Toxic Amyloid Small Oligomer

(2012) Arthur Laganowsky et al.   SCIENCE

β-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel

(2012) Ulrich Zachariae et al.   STRUCTURE

Peptide and protein-based nanotubes for nanobiotechnology

(2012) Anna Petrov et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail

(2011) Carsten Kutzner et al.   BIOPHYSICAL JOURNAL

Alternative packing modes leading to amyloid polymorphism in five fragments studied with molecular dynamics

(2011) Workalemahu M. Berhanu et al.   BIOPOLYMERS

Molecular dynamic simulation of wild type and mutants of the polymorphic amyloid NNQNTF segments of elk prion: Structural stability and thermodynamic of association

(2011) Workalemahu M. Berhanu et al.   BIOPOLYMERS

Amyloid-like Aggregates Sequester Numerous Metastable Proteins with Essential Cellular Functions

(2011) Heidi Olzscha et al.   CELL

Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants

(2011) Workalemahu Mikre Berhanu et al.   JOURNAL OF MOLECULAR MODELING

Controlling the aggregation and rate of release in order to improve insulin formulation: molecular dynamics study of full-length insulin amyloid oligomer models

(2011) Workalemahu Mikre Berhanu et al.   JOURNAL OF MOLECULAR MODELING

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

(2011) Stuart A. Sievers et al.   NATURE

Can molecular dynamics simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN

(2010) Workalemahu Mikre Berhanu et al.   JOURNAL OF MOLECULAR MODELING

In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Misfolding Induced by Frustration of the Salt Bridge Network

(2010) Jinghui Luo et al.   PLoS Computational Biology

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

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

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

Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine

(2009) Jiyong Park et al.   PLoS Computational Biology

Salt-Specific Stability and Denaturation of a Short Salt-Bridge-Forming α-Helix

(2008) Joachim Dzubiella   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