Опубликована: Янв. 1, 2024
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Язык: Английский
Journal of Computational Physics, Год журнала: 2025, Номер unknown, С. 113733 - 113733
Опубликована: Янв. 1, 2025
Язык: Английский
Процитировано
2
The Journal of Chemical Physics, Год журнала: 2024, Номер 160(3)
Опубликована: Янв. 16, 2024
The computational bottleneck of molecular dynamics is pairwise additive long-range interactions between particles. random batch Ewald (RBE) method provides a highly efficient and superscalable solver for interactions, but the stochastic nature this algorithm leads to unphysical self-heating effect during simulation. We propose an energy stable scheme (ESS) particle systems by employing Berendsen-type bath. removes notorious drift, which exists due force error even when symplectic integrator employed. Combining RBE with ESS, new perfect solution at microcanonical ensemble. Numerical results primitive electrolyte all-atom pure water demonstrate attractive performance algorithm, including its dramatically high accuracy, linear complexity, overcoming drift long-time simulations.
Язык: Английский
Процитировано
3
Journal of Chemical Theory and Computation, Год журнала: 2025, Номер unknown
Опубликована: Июнь 3, 2025
The
introduction
of
the
infinite
boundary
terms
and
pairwise
interactions
[Hu,
Z.
J.
Chem.
Theory
Comput.
2014,
10,
5254-5264]
enables
a
physically
intuitive
approach
for
deriving
electrostatic
energy
pressure
both
neutral
non-neutral
systems
under
periodic
condition
(PBC).
For
system
consisting
N
point
charges
(with
charge
qj
located
at
rj
where
j
=
1,
2,
···,
N)
one
distribution
density
ρ(r)
within
primary
cell
volume
V,
derived
can
be
expressed
as,
Σi
Язык: Английский
Процитировано
Energy,
Год журнала:
2023,
Номер
286, С. 129633 - 129633
Опубликована: Ноя. 10, 2023
Язык: Английский
Процитировано
Surfaces and Interfaces,
Год журнала:
2023,
Номер
44, С. 103805 - 103805
Опубликована: Дек. 23, 2023
Язык: Английский
Процитировано
Journal of Biomolecular Structure and Dynamics,
Год журнала:
2024,
Номер
unknown, С. 1 - 19
Опубликована: Янв. 4, 2024
Cyclin-dependent
kinases
(CDKs)
play
a
pivotal
role
in
orchestrating
the
intricate
regulation
of
cell
cycle,
fundamental
process
governing
growth
and
division.
In
particular,
CDK4
CDK6
are
critical
for
transition
from
G1
phase
to
S
phase,
where
Deoxyribonucleic
acid
(DNA)
replication
occurs,
their
dysregulation
is
linked
various
diseases,
notably
cancer.
While
ATP-binding
site
inhibitors
CDKs
well-documented,
this
study
focuses
on
uncovering
allosteric
inhibitors,
providing
fresh
perspective
CDK
inhibition.
Computational
techniques
were
employed
investigation,
utilizing
Molecular
Operating
Environment
(MOE)
virtual
screening
drug-like
compound
library.
Moreover,
stability
most
promising
binding
was
assessed
through
Dynamics
(MD)
simulations
MMPBSA/MMGBSA
analyses.
The
outcome
reveals
that
three
(C1,
C2,
C3)
exhibited
strongest
affinity
CDK4/CDK6,
as
corroborated
by
docking
simulation
computed
energies
ranged
−6.1
−7.6
kcal/mol,
underscoring
potency
these
inhibitors.
Notably,
identifies
key
residues
(PHE31,
HIS95,
HIS100,
VAL101,
ASP102,
ASP104,
THR107)
roles
mediating
inhibitor
within
sites.
Among
findings,
C1–CDK4
complex
C2–CDK6
emerge
particularly
exhibiting
high
energies,
favorable
interaction
patterns,
sustained
presence
active
site.
This
contributes
significantly
pursuit
multi-target
drugs
against
CDK4/CDK6
proteins,
with
potential
implications
development
innovative
therapies
across
disorders,
including
cancer
other
cycle-related
conditions.
Язык: Английский
Процитировано Опубликована: Янв. 1, 2024
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Язык: Английский
Процитировано
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Computational exploration of allosteric inhibitors targeting CDK4/CDK6 proteins: a promising approach for multi-target drug development
Fast Algorithm for Quasi-2d Coulomb Systems