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Unlabelled: Atomic coordinate models are important in the interpretation of 3D maps produced with cryoEM and sub-tomogram averaging in cryoET, or more generically, 3D electron microscopy (3DEM). In addition to visual inspection of such maps and models, quantitative metrics convey the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well-fitted models.
View Article and Find Full Text PDFAn easy-to-use three-dimensional protein-structure-prediction online platform "DPL3D" based on deep learning algorithms.
Curr Res Struct Biol
June 2025
The College of Health Humanities, Jinzhou Medical University, Jinzhou, 121001, China.
The change in the three-dimensional (3D) structure of a protein can affect its own function or interaction with other protein(s), which may lead to disease(s). Gene mutations, especially missense mutations, are the main cause of changes in protein structure. Due to the lack of protein crystal structure data, about three-quarters of human mutant proteins cannot be predicted or accurately predicted, and the pathogenicity of missense mutations can only be indirectly evaluated by evolutionary conservation.
View Article and Find Full Text PDFEngineering a Novel NIR RNA-Specific Probe for Tracking Stress Granule Dynamics in Living Cells.
Anal Chem
January 2025
Institute of Physical Science and Information Technology, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei, Anhui 230601, China.
Real-time monitoring of the dynamics of cytosolic RNA-protein condensates, termed stress granules (SGs), is vital for understanding their biological roles in stress response and related disease treatment but is challenging due to the lack of simple and accurate methods. Compared with protein visualization that requires complex transfection procedures, direct RNA labeling offers an ideal alternative for tracking SG dynamics in living cells. Here, we propose a novel molecular design strategy to construct a near-infrared RNA-specific fluorescent probe () for tracking SGs in living cells.
View Article and Find Full Text PDFA Study of Halide Ion Exchange-Induced Phase Transition in CsPbBr Perovskite Quantum Dots for Detecting Chlorinated Volatile Compounds.
ACS Appl Mater Interfaces
January 2025
Department of Materials Science and Engineering, Feng Chia University, Taichung City, 40724, Taiwan.
The unique optical properties of perovskite quantum dots (PQDs), particularly the tunable photoluminescence (PL) across the visible spectrum, make them a promising tool for chlorinated detection. However, the correlation between the fluorescence emission shift behavior and the interface of phase transformation in PQDs has not been thoroughly explored. In this study, we synthesized CsPbBr PQDs via the hot-injection method and demonstrated their ability to detect chlorinated volatile compounds such as HCl and NaOCl through a halide exchange process between the PQDs' solid thin film and the chlorinated vapor phase.
View Article and Find Full Text PDFUnderstanding drug solubilization in intestinal mixed micelles through molecular dynamics simulations.
J Colloid Interface Sci
April 2025
Department of Chemical and Pharmaceutical Engineering, Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria.
Hypothesis: Solubilization is a fundamental process that underpins various technologies in the pharmaceutical and chemical industry. However, knowledge of the location, orientation and interactions of solubilized molecules in the micelles is still limited. We expect all-atom molecular dynamics simulations to improve the molecular-level understanding of solubilization and to enable its in silico prediction.
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