GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
GENESIS (Generalized‐Ensemble Simulation System) is a new software package for
molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called …
molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called …
Molecular dynamics simulation studies on the aggregation of amyloid-β peptides and their disaggregation by ultrasonic wave and infrared laser irradiation
Alzheimer's disease is understood to be caused by amyloid fibrils and oligomers formed by
aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) …
aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) …
Finding our way in the dark proteome
A Bhowmick, DH Brookes, SR Yost… - Journal of the …, 2016 - ACS Publications
The traditional structure–function paradigm has provided significant insights for well-folded
proteins in which structures can be easily and rapidly revealed by X-ray crystallography …
proteins in which structures can be easily and rapidly revealed by X-ray crystallography …
Perspective for Molecular Dynamics Simulation Studies of Amyloid-β Aggregates
H Okumura - The Journal of Physical Chemistry B, 2023 - ACS Publications
The cause of Alzheimer's disease is related to aggregates such as oligomers and amyloid
fibrils consisting of amyloid-β (Aβ) peptides. Molecular dynamics (MD) simulation studies …
fibrils consisting of amyloid-β (Aβ) peptides. Molecular dynamics (MD) simulation studies …
Role of water molecules and helix structure stabilization in the laser-induced disruption of amyloid fibrils observed by nonequilibrium molecular dynamics simulations
Water plays a crucial role in the formation and destruction of biomolecular structures. The
mechanism for destroying biomolecular structures was thought to be an active breaking of …
mechanism for destroying biomolecular structures was thought to be an active breaking of …
Replica-permutation molecular dynamics simulations of an amyloid-β (16–22) peptide and polyphenols
Aggregates of amyloid-β (Aβ) peptides, such as oligomers and amyloid fibrils, are related to
Alzheimer's disease. Polyphenols are known to inhibit the aggregation of Aβ peptides. We …
Alzheimer's disease. Polyphenols are known to inhibit the aggregation of Aβ peptides. We …
Dynamic properties of SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases studied by molecular dynamics simulations
One of the promising drug targets against COVID-19 is an RNA-dependent RNA polymerase
(RdRp) of SARS-CoV-2. The tertiary structures of the SARS-CoV-2 and SARS-CoV RdRps …
(RdRp) of SARS-CoV-2. The tertiary structures of the SARS-CoV-2 and SARS-CoV RdRps …
Hamiltonian replica‐permutation method and its applications to an alanine dipeptide and amyloid‐β (29–42) peptides
We propose the Hamiltonian replica‐permutation method (RPM)(or multidimensional RPM)
for molecular dynamics and Monte Carlo simulations, in which parameters in the …
for molecular dynamics and Monte Carlo simulations, in which parameters in the …
Dimerization process of amyloid-β (29–42) studied by the Hamiltonian replica-permutation molecular dynamics simulations
The amyloid-β peptides form amyloid fibrils which are associated with Alzheimer's disease.
Amyloid-β (29–42) is its C-terminal fragment and a critical determinant of the amyloid …
Amyloid-β (29–42) is its C-terminal fragment and a critical determinant of the amyloid …
State-of-the-art molecular dynamics simulation studies of RNA-dependent RNA polymerase of SARS-CoV-2
Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal
biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of …
biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of …