Enhanced sampling strategies for molecular simulation of DNA
Molecular dynamics (MD) simulations can provide detailed insights into complex molecular
systems, such as DNA, at high resolution in space and time. Using current computer …
systems, such as DNA, at high resolution in space and time. Using current computer …
YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition
M Ikei, R Miyazaki, K Monden, Y Naito, A Takeuchi… - Plos …, 2024 - journals.plos.org
Uptake of thiosulfate ions as an inorganic sulfur source from the environment is important for
bacterial sulfur assimilation. Recently, a selective thiosulfate uptake pathway involving a …
bacterial sulfur assimilation. Recently, a selective thiosulfate uptake pathway involving a …
SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine
We present SEEKR2 (simulation-enabled estimation of kinetic rates version 2)─ the latest
iteration in the family of SEEKR programs for using multiscale simulation methods to …
iteration in the family of SEEKR programs for using multiscale simulation methods to …
Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment
JT Linzer, E Aminov, AS Abdullah… - Journal of Chemical …, 2024 - ACS Publications
Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in
solution, with stem-loops being one of the more common motifs. Here, we present a …
solution, with stem-loops being one of the more common motifs. Here, we present a …
Modified protein-water interactions in CHARMM36m for thermodynamics and kinetics of proteins in dilute and crowded solutions
Proper balance between protein-protein and protein-water interactions is vital for atomistic
molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered …
molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered …
AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex
Protein translocation across cellular membranes is an essential and nano-scale dynamic
process. In the bacterial cytoplasmic membrane, the core proteins in this process are a …
process. In the bacterial cytoplasmic membrane, the core proteins in this process are a …
Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process
Molecular dynamics (MD) simulation of biologically relevant processes at realistic time scale
and atomistic precision is generally limited by prohibitively large computational cost, due to …
and atomistic precision is generally limited by prohibitively large computational cost, due to …
Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR …
K Watanabe, Q Zhao, R Iwatsuki, R Fukui… - Journal of the …, 2024 - ACS Publications
HDM2 negatively regulates the activity of the tumor suppressor p53. Previous NMR studies
have shown that apo-HDM2 interconverts between an “open” state in which the N-terminal …
have shown that apo-HDM2 interconverts between an “open” state in which the N-terminal …
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer
Generalized replica exchange with solute tempering (gREST) is one of the enhanced
sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike …
sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike …
Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations
Software for accurate prediction of protein-ligand binding affinity can be a key enabling tool
for small molecule drug discovery. Free energy perturbation (FEP) is a computational …
for small molecule drug discovery. Free energy perturbation (FEP) is a computational …