Journal of visualized experiments : JoVE
Nov 11, 2022
Cryo-electron tomography (cryo-ET) allows researchers to image cells in their native, hydrated state at the highest resolution currently possible. The technique has several limitations, however, that make analyzing the data it generates time-intensiv...
Faraday discussions
Nov 8, 2022
During the past 10 years, biological electron cryo-microscopy (cryoEM) has undergone a process of rapid transformation. Many things we could only dream about a decade ago have now become almost routine. Nevertheless, a number of challenges remain, to...
Journal of chemical theory and computation
Nov 1, 2022
We present two machine learning methodologies that are capable of predicting diffusion Monte Carlo (DMC) energies with small data sets (≈60 DMC calculations in total). The first uses voxel deep neural networks (VDNNs) to predict DMC energy densities ...
Physical chemistry chemical physics : PCCP
Sep 21, 2022
We provide a comprehensive overview of the chemical information from electron density: not only how to extract information, but also how to obtain and how to assess the quality of the electron density itself. After introducing several indexes derived...
Physics in medicine and biology
Sep 15, 2022
. Obtaining the intrinsic dose distributions in particle therapy is a challenging problem that needs to be addressed by imaging algorithms to take advantage of secondary particle detectors. In this work, we investigate the utility of deep learning me...
BMC bioinformatics
Aug 30, 2022
BACKGROUND: Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexit...
Scientific reports
Aug 24, 2022
Predicting material properties by solving the Kohn-Sham (KS) equation, which is the basis of modern computational approaches to electronic structures, has provided significant improvements in materials sciences. Despite its contributions, both DFT an...
Computer methods and programs in biomedicine
Jul 1, 2022
BACKGROUND AND OBJECTIVE: Cryo-electron tomography (cryo-ET) is an imaging technique that enables 3D visualization of the native cellular environment at sub-nanometer resolution, providing unpreceded insights into the molecular organization of cells....
Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)
Jun 9, 2022
PURPOSE: Proton-induced secondary-electron-bremsstrahlung (SEB) imaging is a promising method for estimating the ranges of particle beam. However, SEB images do not directly represent dose distributions of particle beams. In addition, the ranges esti...
Journal of chemical information and modeling
Mar 29, 2022
We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling of noncovalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on reduced electron density gradient (RDG) theo...