AIMC Topic: Macromolecular Substances

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Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein-Ligand Interaction Research.

Journal of chemical information and modeling
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...

Bayesian deep learning-based H-MRS of the brain: Metabolite quantification with uncertainty estimation using Monte Carlo dropout.

Magnetic resonance in medicine
PURPOSE: To develop a Bayesian convolutional neural network (BCNN) with Monte Carlo dropout sampling for metabolite quantification with simultaneous uncertainty estimation in deep learning-based proton MRS of the brain.

Macromolecules Structural Classification With a 3D Dilated Dense Network in Cryo-Electron Tomography.

IEEE/ACM transactions on computational biology and bioinformatics
Cryo-electron tomography, combined with subtomogram averaging (STA), can reveal three-dimensional (3D) macromolecule structures in the near-native state from cells and other biological samples. In STA, to get a high-resolution 3D view of macromolecul...

Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms.

Nature methods
Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and rec...

Magneto-Responsive Microneedle Robots for Intestinal Macromolecule Delivery.

Advanced materials (Deerfield Beach, Fla.)
Oral administration is the most convenient and commonly used approach for drug delivery, while it is still a challenge to overcome the complicated gastrointestinal barriers and realize efficient macromolecular drug absorption. Here, novel magneto-res...

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II.

Journal of synchrotron radiation
Here we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated una...

Deep Learning of Binary Solution Phase Behavior of Polystyrene.

ACS macro letters
Predicting binary solution phase behavior of polymers has remained a challenge since the early theory of Flory-Huggins, hindering the processing, synthesis, and design of polymeric materials. Herein, we take a complementary data-driven approach by bu...

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.

Nature methods
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many imaged protein complexes exhibit conformational and compositional heterogeneity that poses a major ch...

MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning.

Journal of structural biology
Cryo-EM Single Particle Analysis workflows require tens of thousands of high-quality particle projections to unveil the three-dimensional structure of macromolecules. Conventional methods for automatic particle picking tend to suffer from high false-...

A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation.

Journal of structural biology
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isola...