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Computational Studies of Protein Aggregation: Methods and Applications

Annual review of physical chemistry, 2015-04, Vol.66 (1), p.643-666

2015

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Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions

eLife, 2019-04, Vol.8

2019

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Liquid–liquid phase separation of Tau by self and complex coacervation

Protein science, 2021-07, Vol.30 (7), p.1393-1407

2021

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CORE-MD, a path correlated molecular dynamics simulation method

The Journal of chemical physics, 2020-08, Vol.153 (8), p.084114-084114

2020

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Dehydration entropy drives liquid-liquid phase separation by molecular crowding

Communications chemistry, 2020-06, Vol.3 (1), p.83-83, Article 83

2020

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Diversity of kinetic pathways in amyloid fibril formation

The Journal of chemical physics, 2009-09, Vol.131 (11), p.111102-111102-4

2009

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Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

Journal of the American Chemical Society, 2014-10, Vol.136 (39), p.13582-13585

2014

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An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation

Physical chemistry chemical physics : PCCP, 2017, Vol.19 (26), p.17373-17382

2017

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Coarse-grained models for protein aggregation

Current opinion in structural biology, 2011-04, Vol.21 (2), p.209-220

2011

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Double Resolution Model for Studying TMAO/Water Effective Interactions

The journal of physical chemistry. B, 2013-10, Vol.117 (42), p.13268-13277

2013

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Amyloid β‐protein monomer structure: A computational and experimental study

Protein science, 2006-03, Vol.15 (3), p.420-428

2006

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A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

The Journal of chemical physics, 2015-04, Vol.142 (14), p.144903-144903

2015

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Sequence periodicity and secondary structure propensity in model proteins

Protein science, 2010-01, Vol.19 (1), p.141-154

2010

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Effect of β -sheet propensity on peptide aggregation

The Journal of chemical physics, 2009-04, Vol.130 (14), p.145103-145103-10

2009

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Relative stability of de novo four–helix bundle proteins: Insights from coarse grained molecular simulations

Protein science, 2011-05, Vol.20 (5), p.818-826

2011

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Self-assembly of β -sheet forming peptides into chiral fibrillar aggregates

The Journal of chemical physics, 2007-06, Vol.126 (24), p.245104-245104-11

2007

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Effects of Solvent on the Structure of the Alzheimer Amyloid-β(25–35) Peptide

Biophysical journal, 2006-09, Vol.91 (5), p.1638-1647

2006

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The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

Journal of molecular biology, 2007-02, Vol.366 (1), p.275-285

2007

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The Influence of Different Treatments of Electrostatic Interactions on the Thermodynamics of Folding of Peptides

The journal of physical chemistry. B, 2005-11, Vol.109 (45), p.21322-21328

2005

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Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

Physical chemistry chemical physics : PCCP, 2016-05, Vol.18 (18), p.1352-1365

2016

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Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling

The journal of physical chemistry. B, 2012-07, Vol.116 (29), p.8337-8349

2012

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New Insights into the Mechanism of Alzheimer Amyloid- β Fibrillogenesis Inhibition by N-Methylated Peptides

Biophysical journal, 2007-11, Vol.93 (9), p.3015-3025

2007

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Posttransition State Desolvation of the Hydrophobic Core of the src-SH3 Protein Domain

Biophysical journal, 2003-07, Vol.85 (1), p.61-69

2003

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Stability of a protein tethered to a surface

The Journal of chemical physics, 2007-03, Vol.126 (9), p.095101-095101-12

2007

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Temperature dependence of the free energy landscape of the src-SH3 protein domain

Proteins, structure, function, and bioinformatics, 2004-05, Vol.55 (2), p.395-406

2004

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Computational Studies of Protein Aggregation: Methods and Applications

Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions

Liquid–liquid phase separation of Tau by self and complex coacervation

CORE-MD, a path correlated molecular dynamics simulation method

Dehydration entropy drives liquid-liquid phase separation by molecular crowding

Diversity of kinetic pathways in amyloid fibril formation

Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation

Coarse-grained models for protein aggregation

Double Resolution Model for Studying TMAO/Water Effective Interactions

Amyloid β‐protein monomer structure: A computational and experimental study

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

Sequence periodicity and secondary structure propensity in model proteins

Effect of β -sheet propensity on peptide aggregation

Relative stability of de novo four–helix bundle proteins: Insights from coarse grained molecular simulations

Self-assembly of β -sheet forming peptides into chiral fibrillar aggregates

Effects of Solvent on the Structure of the Alzheimer Amyloid-β(25–35) Peptide

The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

The Influence of Different Treatments of Electrostatic Interactions on the Thermodynamics of Folding of Peptides

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling

New Insights into the Mechanism of Alzheimer Amyloid- β Fibrillogenesis Inhibition by N-Methylated Peptides

Posttransition State Desolvation of the Hydrophobic Core of the src-SH3 Protein Domain

Stability of a protein tethered to a surface

Temperature dependence of the free energy landscape of the src-SH3 protein domain

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