Stability of Iowa mutant and wild type Aβ-peptide aggregates

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Effect of D23N mutation on the dimer conformation of amyloid β-proteins: Ab initio molecular simulations in water

(2014) Akisumi Okamoto et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Cell-to-cell transmission of pathogenic proteins in neurodegenerative diseases

(2014) Jing L Guo et al.   NATURE MEDICINE

Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy

(2014) L. E. Buchanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physical and structural basis for polymorphism in amyloid fibrils

(2014) Robert Tycko   PROTEIN SCIENCE

In Silico Cross Seeding of Aβ and Amylin Fibril-like Oligomers

(2013) Workalemahu M. Berhanu et al.   ACS Chemical Neuroscience

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates

(2013) Mohamed Raef Smaoui et al.   BIOPHYSICAL JOURNAL

Mutations and Seeding of Amylin Fibril-Like Oligomers

(2013) Nathan A Bernhardt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide

(2013) Louise B. Wright et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Conformational Stability of Fibrillar Amyloid-Beta Oligomers via Protofilament Pair Formation – A Systematic Computational Study

(2013) Anna Kahler et al.   PLoS One

Atomic structure and hierarchical assembly of a cross-  amyloid fibril

(2013) A. W. P. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Workalemahu M. Berhanu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta

(2013) Lin Jiang et al.   eLife

Hydrogen Bonding in Alzheimer’s Amyloid-β Fibrils Probed by15N{17O} REAPDOR Solid-State NMR Spectroscopy

(2012) Oleg N. Antzutkin et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Amyloid State of Proteins in Human Diseases

(2012) David Eisenberg et al.   CELL

Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane

(2012) Hyunbum Jang et al.   Journal of Chemical Theory and Computation

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

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

Peptide Chain Dynamics in Light and Heavy Water: Zooming in on Internal Friction

(2012) Julius C. F. Schulz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

Structure and Dynamics of Amyloid-β Segmental Polymorphisms

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

Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study

(2012) Dimitrios Spiliotopoulos et al.   PLoS One

Antiparallel  -sheet architecture in Iowa-mutant  -amyloid fibrils

(2012) W. Qiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Solid-State NMR Studies of Amyloid Fibril Structure

(2011) Robert Tycko   Annual Review of Physical Chemistry

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

(2011) Carsten Kutzner et al.   BIOPHYSICAL JOURNAL

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

The Unique Alzheimer’s β-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions

(2011) Yifat Miller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions

(2010) Jun Zhao et al.   BIOMACROMOLECULES

Polymorphism in Alzheimer Aβ Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape

(2010) Yifat Miller et al.   CHEMICAL REVIEWS

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

(2010) I-Chun Lin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils

(2010) Mahiuddin Ahmed et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evidence for Novel β-Sheet Structures in Iowa Mutant β-Amyloid Fibrils

(2009) Robert Tycko et al.   BIOCHEMISTRY

Polymorphism of Alzheimer's Aβ17-42 (p3) Oligomers: The Importance of the Turn Location and Its Conformation

(2009) Yifat Miller et al.   BIOPHYSICAL JOURNAL

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

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

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

(2009) Jiyong Park et al.   PLoS Computational Biology

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation