OpenMM 8: molecular dynamics simulation with machine learning potentials
P Eastman, R Galvelis, RP Peláez… - The Journal of …, 2023 - ACS Publications
Machine learning plays an important and growing role in molecular simulation. The newest
version of the OpenMM molecular dynamics toolkit introduces new features to support the …
version of the OpenMM molecular dynamics toolkit introduces new features to support the …
Expanding the molecular language of protein liquid–liquid phase separation
Understanding the relationship between a polypeptide sequence and its phase separation
has important implications for analysing cellular function, treating disease and designing …
has important implications for analysing cellular function, treating disease and designing …
Mechanochemically accelerated deconstruction of chemically recyclable plastics
Plastics redesign for circularity has primarily focused on monomer chemistries enabling
faster deconstruction rates concomitant with high monomer yields. Yet, during …
faster deconstruction rates concomitant with high monomer yields. Yet, during …
A Zn‐dependent structural transition of SOD1 modulates its ability to undergo phase separation
The misfolding and mutation of Cu/Zn superoxide dismutase (SOD1) is commonly
associated with amyotrophic lateral sclerosis (ALS). SOD1 can accumulate within stress …
associated with amyotrophic lateral sclerosis (ALS). SOD1 can accumulate within stress …
Machine-learned molecular mechanics force fields from large-scale quantum chemical data
The development of reliable and extensible molecular mechanics (MM) force fields—fast,
empirical models characterizing the potential energy surface of molecular systems—is …
empirical models characterizing the potential energy surface of molecular systems—is …
Rigid body flows for sampling molecular crystal structures
Normalizing flows (NF) are a class of powerful generative models that have gained
popularity in recent years due to their ability to model complex distributions with high …
popularity in recent years due to their ability to model complex distributions with high …
A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP‐43 and modulates its phase behavior
Abstract TAR DNA‐binding protein 43 (TDP‐43) is a multidomain protein involved in the
regulation of RNA metabolism, and its aggregates have been observed in …
regulation of RNA metabolism, and its aggregates have been observed in …
Stable amorphous solid dispersion of flubendazole with high loading via electrospinning
J Becelaere, E Van Den Broeck, E Schoolaert… - Journal of Controlled …, 2022 - Elsevier
In this work, an important step is taken towards the bioavailability improvement of poorly
water-soluble drugs, such as flubendazole (Flu), posing a challenge in the current …
water-soluble drugs, such as flubendazole (Flu), posing a challenge in the current …
Automated adaptive absolute binding free energy calculations
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in
drug discovery, but are often prohibitively computationally expensive. To unlock their …
drug discovery, but are often prohibitively computationally expensive. To unlock their …
Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding
Heterochromatin protein 1α (HP1α) is a crucial element of chromatin organization. It has
been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which …
been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which …