Equilibrium sampling in biomolecular simulations
DM Zuckerman - Annual review of biophysics, 2011 - annualreviews.org
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years
of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here …
of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here …
Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms
J Shao, SW Tanner, N Thompson… - Journal of chemical …, 2007 - ACS Publications
Molecular dynamics simulation methods produce trajectories of atomic positions (and
optionally velocities and energies) as a function of time and provide a representation of the …
optionally velocities and energies) as a function of time and provide a representation of the …
[HTML][HTML] Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: a mini-review
The molecular dynamics (MD) method is a promising approach toward elucidating the
molecular mechanisms of intrinsically disordered regions (IDRs) of proteins and their fuzzy …
molecular mechanisms of intrinsically disordered regions (IDRs) of proteins and their fuzzy …
Carbon nanotube inhibits the formation of β-sheet-rich oligomers of the Alzheimer's amyloid-β (16-22) peptide
H Li, Y Luo, P Derreumaux, G Wei - Biophysical journal, 2011 - cell.com
Alzheimer's disease is associated with the abnormal self-assembly of the amyloid-β (Aβ)
peptide into toxic β-rich aggregates. Experimental studies have shown that hydrophobic …
peptide into toxic β-rich aggregates. Experimental studies have shown that hydrophobic …
Replica exchange molecular dynamics: a practical application protocol with solutions to common problems and a peptide aggregation and self-assembly example
Protein aggregation is associated with many human diseases such as Alzheimer's disease
(AD), Parkinson's disease (PD), and type II diabetes (T2D). Understanding the molecular …
(AD), Parkinson's disease (PD), and type II diabetes (T2D). Understanding the molecular …
Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome
J Šponer, P Banáš, P Jurecka… - The journal of …, 2014 - ACS Publications
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …
Multidimensional replica exchange molecular dynamics yields a converged ensemble of an RNA tetranucleotide
A necessary step to properly assess and validate the performance of force fields for
biomolecules is to exhaustively sample the accessible conformational space, which is …
biomolecules is to exhaustively sample the accessible conformational space, which is …
Rapid equilibrium sampling initiated from nonequilibrium data
Simulating the conformational dynamics of biomolecules is extremely difficult due to the
rugged nature of their free energy landscapes and multiple long-lived, or metastable, states …
rugged nature of their free energy landscapes and multiple long-lived, or metastable, states …
Demonstrating an order-of-magnitude sampling enhancement in molecular dynamics simulations of complex protein systems
Molecular dynamics (MD) simulations can describe protein motions in atomic detail, but
transitions between protein conformational states sometimes take place on time scales that …
transitions between protein conformational states sometimes take place on time scales that …
Exchange often and properly in replica exchange molecular dynamics
Previous work by us showed that in replica exchange molecular dynamics, exchanges
should be attempted extremely often, providing gains in efficiency and no undesired effects …
should be attempted extremely often, providing gains in efficiency and no undesired effects …