Related references
Note: Only part of the references are listed.Scalable molecular dynamics on CPU and GPU architectures with NAMD
James C. Phillips et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates
Ioana M. Ilie et al.
CHEMICAL REVIEWS (2019)
Markov State Models: From an Art to a Science
Brooke E. Husic et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)
In Silico Crystal Growth Rate Prediction for NaCl from Aqueous Solution
Mark N. Joswiak et al.
CRYSTAL GROWTH & DESIGN (2018)
Nonproductive Binding Modes as a Prominent Feature of Aβ40 Fiber Elongation: Insights from Molecular Dynamics Simulation
Rajiv K. Kar et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes
Zahra Shamsi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State
Roberto A. Rodriguez et al.
ACS CHEMICAL NEUROSCIENCE (2018)
Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip
Marco Bacci et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix
Sunita Patel et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Nuria Plattner et al.
NATURE CHEMISTRY (2017)
Imaging Aβ(1-42) fibril elongation reveals strongly polarised growth and growth incompetent states
Laurence J. Young et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
Reaction Coordinates and Mechanistic Hypothesis Tests
Baron Peters
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 67 (2016)
Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation
Andela Saric et al.
JOURNAL OF CHEMICAL PHYSICS (2016)
Mechanism of Nucleation and Growth of Aβ40 Fibrils from All-Atom and Coarse-Grained Simulations
Sukanya Sasmal et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step
Nadine Schwierz et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
Recent advances in coarse-grained modeling of virus assembly
Michael F. Hagan et al.
CURRENT OPINION IN VIROLOGY (2016)
The Statistical Mechanics of Dynamic Pathways to Self-Assembly
Stephen Whitelam et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 66 (2015)
Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps
Lorenzo Boninsegna et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models
Marieke Schor et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2015)
Mechanism of Amyloid-β Fibril Elongation
Thomas Gurry et al.
BIOCHEMISTRY (2014)
Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations
Michel A. Cuendet et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Fibril Elongation by Aβ17-42: Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations
Wei Han et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
Impact of sequence on the molecular assembly of short amyloid peptides
Victoria A. Wagoner et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2014)
Charge Effects on the Fibril-Forming Peptide KTVIIE: A Two-Dimensional Replica Exchange Simulation Study
Joohyun Jeon et al.
BIOPHYSICAL JOURNAL (2012)
Elucidating the Locking Mechanism of Peptides onto Growing Amyloid Fibrils through Transition Path Sampling
Marieke Schor et al.
BIOPHYSICAL JOURNAL (2012)
Two-Step Nucleation of Amyloid Fibrils: Omnipresent or Not?
Stefan Auer et al.
JOURNAL OF MOLECULAR BIOLOGY (2012)
Toward a Molecular Theory of Early and Late Events in Monomer to Amyloid Fibril Formation
John E. Straub et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 62 (2011)
What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils?
Jeremy D. Schmit et al.
BIOPHYSICAL JOURNAL (2011)
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
Nathan Schmid et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)
Atomistic theory of amyloid fibril nucleation
Raffaela Cabriolu et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Nucleation of amyloid fibrils
Dimo Kashchiev et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field
Ana Rojas et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Replica Exchange Simulations of the Thermodynamics of Aβ Fibril Growth
Takako Takeda et al.
BIOPHYSICAL JOURNAL (2009)
Polymorphism of Alzheimer's Aβ17-42 (p3) Oligomers: The Importance of the Turn Location and Its Conformation
Yifat Miller et al.
BIOPHYSICAL JOURNAL (2009)
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Massimiliano Bonomi et al.
COMPUTER PHYSICS COMMUNICATIONS (2009)
Simulations of nucleation and elongation of amyloid fibrils
Jianing Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
CHARMM: The Biomolecular Simulation Program
B. R. Brooks et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Thermodynamic Perspective on the Dock-Lock Growth Mechanism of Amyloid Fibrils
Edward P. O'Brien et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Elongation dynamics of amyloid fibrils: A rugged energy landscape picture
Chiu Fan Lee et al.
PHYSICAL REVIEW E (2009)
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Frank Noe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
An Analytical Solution to the Kinetics of Breakable Filament Assembly
Tuomas P. J. Knowles et al.
SCIENCE (2009)
Adaptive biasing force method for scalar and vector free energy calculations
Eric Darve et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates
Giovanni Bellesia et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Aβ1-40 peptide
Nicolas Lux Fawzi et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism
Phuong H. Nguyen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Interpreting the aggregation kinetics of amyloid peptides
Riccardo Pellarin et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Dynamic pathways for viral capsid assembly
Michael F. Hagan et al.
BIOPHYSICAL JOURNAL (2006)
Forward flux sampling-type schemes for simulating rare events: Efficiency analysis
Rosalind J. Allen et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
P versus Q:: Structural reaction coordinates capture protein folding on smooth landscapes
SS Cho et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Kinetic analysis of beta-amyloid fibril elongation
MJ Cannon et al.
ANALYTICAL BIOCHEMISTRY (2004)
Inter-residue interactions in protein folding and stability
MM Gromiha et al.
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2004)
A novel path sampling method for the calculation of rate constants
TS van Erp et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
An algorithmic introduction to numerical simulation of stochastic differential equations
DJ Higham
SIAM REVIEW (2001)
Protein folding: progress made and promises ahead
SE Radford
TRENDS IN BIOCHEMICAL SCIENCES (2000)
Alzheimer's disease amyloid propagation by a template-dependent dock-lock mechanism
WP Esler et al.
BIOCHEMISTRY (2000)
Share Paper
