AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics.

All-atom molecular simulations offer detailed insights into macromolecular phenomena, but their substantial computational cost hinders the exploration of complex biological processes. We introduce Advanced Machine-learning Atomic Representation Omni-force-field (AMARO), a new neural network potential (NNP) that combines an O(3)-equivariant message-passing neural network architecture, TensorNet, with a coarse-graining map that excludes hydrogen atoms. AMARO demonstrates the feasibility of training coarser NNP, without prior energy terms, to run stable protein dynamics with scalability and generalization capabilities.

Deciphering Chemical Rules for Drug Penetration into Strongyloides.

Strongyloidiasis, a parasitic infection, presents a significant public health challenge in tropical regions due to the limited repertoire of effective treatments. The screening of chemical libraries against the therapeutically relevant third-stage larvae (L3) of the model parasite yielded meager success rates. This situation is reminiscent of Gram-negative bacteria, where drug entry is a limiting factor.

Methylene Blue Reduces Electroretinogram Distortion and Ganglion Cell Death in a Rat Model of Glaucoma.

Glaucoma is the second leading cause of blindness worldwide and is, in most cases, a consequence of elevated intraocular pressure (IOP), ultimately resulting in the death of retinal ganglion cells (RGCs). Current treatments are mostly focused on normalizing IOP, but we propose the additional use of neuroprotective agents, including methylene blue (MB), to block the loss of RGCs. Wistar rats were subjected to episcleral vein cauterization (EVC) in the left eye while the right eye was sham-operated.